count: 49
list:
- accessibility: Open access
  additionDate: '2025-07-23T10:27:57.572501Z'
  biotoolsCURIE: biotools:etenlnc
  biotoolsID: etenlnc
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: barah@tezu.ernet.in
    fundrefid: null
    gridid: null
    name: Pankaj Barah
    note: Assistant Professor at Department of Molecular Biology and Biotechnology,
      Tezpur University.
    orcidid: https://orcid.org/0000-0001-7039-7996
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Maintainer
    url: https://www.tezu.ernet.in/dmbbt/profile/34
  - email: prangannathofficial@gmai.com
    fundrefid: null
    gridid: null
    name: Prangan Nath
    note: null
    orcidid: https://orcid.org/0000-0002-9451-7822
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  description: ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and
    analysis framework
  documentation:
  - note: A detailed guide on running ETENLNC using the demo data can be found in
      the ETENLNC manual (supplementary to our publication)
    type:
    - Command-line options
    url: https://github.com/EvolOMICS-TU/ETENLNC
  download:
  - note: Sample/demo data for ETENLNC. A detailed guide on running ETENLNC using
      the demo data can be found in the ETENLNC manual (supplementary to our publication).
    type: Biological data
    url: https://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnw
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: bash ETENLNC_docker.sh
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GTF
        uri: http://edamontology.org/format_2306
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Run ETENLNC on paired-end raw RNA-Seq (.fastq) data
    operation:
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Transcriptome assembly
      uri: http://edamontology.org/operation_3258
    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    - term: Protein-nucleic acid interaction analysis
      uri: http://edamontology.org/operation_0389
    - term: RNA-binding protein prediction
      uri: http://edamontology.org/operation_3901
    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    output:
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format: []
  homepage: https://github.com/EvolOMICS-TU/ETENLNC
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-23T10:27:57.574879Z'
  license: GPL-3.0
  link:
  - note: GitHub Repo
    type:
    - Repository
    url: https://github.com/EvolOMICS-TU/ETENLNC
  maturity: Emerging
  name: ETENLNC
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: prangannath
  publication:
  - doi: 10.1016/j.compbiolchem.2024.108140
    metadata:
      abstract: 'Long non-coding RNAs (lncRNAs) play crucial roles in the regulation
        of gene expression and maintenance of genomic integrity through various interactions
        with DNA, RNA, and proteins. The availability of large-scale sequence data
        from various high-throughput platforms has opened possibilities to identify,
        predict, and functionally annotate lncRNAs. As a result, there is a growing
        demand for an integrative computational framework capable of identifying known
        lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory
        interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding),
        a user-friendly, integrative, open-source, scalable, and modular computational
        framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC
        employs six stringent filtration steps to identify novel lncRNAs, performs
        differential expression analysis of mRNA and lncRNA transcripts, and predicts
        regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked
        ETENLNC against six existing tools and optimized it for desktop workstations
        and high-performance computing environments using data from three different
        species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.'
      authors:
      - name: Nath P.
      - name: Bhuyan K.
      - name: Bhattacharyya D.K.
      - name: Barah P.
      citationCount: 2
      date: '2024-10-01T00:00:00Z'
      journal: Computational Biology and Chemistry
      title: 'ETENLNC: An end to end lncRNA identification and analysis framework
        to facilitate construction of known and novel lncRNA regulatory networks'
    note: null
    pmcid: null
    pmid: '38996755'
    type:
    - Primary
    version: '.0'
  relation:
  - biotoolsID: hisat2
    type: uses
  - biotoolsID: salmon
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: fastp
    type: uses
  - biotoolsID: stringtie
    type: uses
  - biotoolsID: gffcompare
    type: uses
  - biotoolsID: cpc2
    type: uses
  - biotoolsID: ncbi_blast_plus
    type: uses
  - biotoolsID: tximport
    type: uses
  - biotoolsID: deseq2
    type: uses
  - biotoolsID: lnctar
    type: uses
  - biotoolsID: capsule-lpi
    type: uses
  - biotoolsID: seekr
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - '1.0'
- accessibility: Open access (with restrictions)
  additionDate: '2025-07-10T03:21:50.923918Z'
  biotoolsCURIE: biotools:colopola_dataset_for_colorectal_cancer_detection
  biotoolsID: colopola_dataset_for_colorectal_cancer_detection
  collectionID:
  - Dataset
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit: []
  description: The dataset consists of 572 slices (specimens) with 20,592 images.
    There are 284 cancer samples and 288 normal samples. The lists of samples for
    training (train+val) set and testing set are provided in the Zenodo repository.
    Source code in Github is to train and validate five deep learning models using
    ColoPola dataset.
  documentation: []
  download:
  - note: Python language
    type: Source code
    url: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset
    version: '1.0'
  - note: Dataset for running source code
    type: Test data
    url: https://zenodo.org/records/10554304
    version: '1.2'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-10T03:33:52.616431Z'
  license: CC0-1.0
  link:
  - note: Source code
    type:
    - Repository
    url: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset
  - note: null
    type:
    - Issue tracker
    url: https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset/issues
  maturity: Mature
  name: ColoPola dataset for colorectal cancer detection
  operatingSystem:
  - Windows
  otherID: []
  owner: haile
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2016-04-15T11:52:42Z'
  biotoolsCURIE: biotools:comparems2
  biotoolsID: comparems2
  collectionID:
  - ms-utils
  - Proteomics
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: lumc.nl
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Support
    url: https://www.lumc.nl
  - email: magnus.palmblad@gmail.com
    fundrefid: null
    gridid: null
    name: Magnus Palmblad
    note: null
    orcidid: http://orcid.org/0000-0002-5865-8994
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Documentor
    url: https://github.com/magnuspalmblad
  - email: null
    fundrefid: null
    gridid: null
    name: Rob Marissen
    note: null
    orcidid: https://orcid.org/0000-0002-1220-9173
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/524D
  description: compareMS2 is a tool for comparing sets of (tandem) mass spectra for
    clustering samples, molecular phylogenetics, identification of biological species
    or tissues, and quality control. compareMS2 currently consumes Mascot Generic
    Format, or MGF, and produces output in a variety of common image and distance
    matrix formats.
  documentation:
  - note: null
    type:
    - General
    - Command-line options
    url: http://www.ms-utils.org/compareMS2.html
  - note: null
    type:
    - General
    - User manual
    - Command-line options
    - Installation instructions
    url: https://github.com/524D/compareMS2
  download:
  - note: null
    type: Source code
    url: http://www.ms-utils.org/compareMS2.c
    version: '1.0'
  - note: null
    type: Binaries
    url: http://www.ms-utils.org/compareMS2.html
    version: '1.0'
  - note: null
    type: Source code
    url: http://www.ms-utils.org/compareMS2.c
    version: '1.0'
  - note: null
    type: Source code
    url: https://github.com/524D/compareMS2/tree/main/src
    version: '2.0'
  - note: null
    type: Binaries
    url: https://github.com/524D/compareMS2/tree/main
    version: '2.0'
  editPermission:
    authors:
    - proteomics.bio.tools
    type: group
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Netherlands
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    output:
    - data:
        term: Species tree
        uri: http://edamontology.org/data_3272
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Distance matrix
        uri: http://edamontology.org/data_2855
      format:
      - term: mega
        uri: http://edamontology.org/format_1991
      - term: Nexus format
        uri: http://edamontology.org/format_1912
      - term: newick
        uri: http://edamontology.org/format_1910
  homepage: https://github.com/524D/compareMS2
  homepage_status: 0
  language:
  - C
  - JavaScript
  lastUpdate: '2025-04-16T14:22:04.957317Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/524D/compareMS2
  - note: null
    type:
    - Software catalogue
    url: https://www.ms-utils.org/compareMS2.html
  - note: null
    type:
    - Software catalogue
    url: https://research-software-directory.org/software/comparems2
  maturity: Mature
  name: compareMS2
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1002/rcm.6162
    metadata:
      abstract: 'Rationale: Molecular phylogenetics is the study of evolution and
        relatedness of organisms or genes. Mass spectrometry is used routinely for
        bacterial identification and has also been used for phylogenetic analysis,
        for instance from bone material. Unfortunately, only a small fraction of the
        acquired tandem mass spectra allow direct interpretation. Methods: We describe
        a new algorithm and software for molecular phylogenetics using pairwise comparisons
        of tandem mass spectra from enzymatically digested proteins. The spectra need
        not be annotated and all acquired data is used in the analysis. To demonstrate
        the method, we analyzed tryptic digests of sera from four great apes and two
        other primates. Results: The distribution of spectra dot products for thousands
        of tandem mass spectra collected from two samples provides a measure on the
        fraction of shared peptides between the two samples. When inverted, this becomes
        a distance metric. By pairwise comparison between species and averaging over
        four individuals per species, it was possible to reconstruct the unique correct
        phylogenetic tree for the great apes and other primates. Conclusions: The
        new method described here has several attractive features compared with existing
        methods, among them simplicity, the unbiased use of all acquired data rather
        than a small subset of spectra, and the potential use of heavily degraded
        proteins or proteins with a priori unknown modifications. © 2012 John Wiley
        & Sons, Ltd.'
      authors:
      - name: Palmblad M.
      - name: Deelder A.M.
      citationCount: 30
      date: '2012-04-15T00:00:00Z'
      journal: Rapid Communications in Mass Spectrometry
      title: Molecular phylogenetics by direct comparison of tandem mass spectra
    note: null
    pmcid: null
    pmid: '22368051'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1021/acs.jproteome.2c00457
    metadata:
      abstract: It has long been known that biological species can be identified from
        mass spectrometry data alone. Ten years ago, we described a method and software
        tool, compareMS2, for calculating a distance between sets of tandem mass spectra,
        as routinely collected in proteomics. This method has seen use in species
        identification and mixture characterization in food and feed products, as
        well as other applications. Here, we present the first major update of this
        software, including a new metric, a graphical user interface and additional
        functionality. The data have been deposited to ProteomeXchange with dataset
        identifier PXD034932.
      authors:
      - name: Marissen R.
      - name: Varunjikar M.S.
      - name: Laros J.F.J.
      - name: Rasinger J.D.
      - name: Neely B.A.
      - name: Palmblad M.
      citationCount: 7
      date: '2023-02-03T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry
        Datasets'
    note: null
    pmcid: PMC9903320
    pmid: '36173614'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1021/acs.jproteome.1c00528
    metadata:
      abstract: Science is full of overlooked and undervalued research waiting to
        be rediscovered. Proteomics is no exception. In this perspective, we follow
        the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing
        tryptic peptides across animal species. This pioneering work directly led
        to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics.
        In the decades following, proteins continued to provide essential clues on
        evolutionary history. While technology has continued to improve, contemporary
        proteomics has strayed from this larger biological context, rarely comparing
        species or asking how protein structure, function, and interactions have evolved.
        Here we recombine proteomics with molecular phylogenetics, highlighting the
        value of framing proteomic results in a larger biological context and how
        almost forgotten research, though technologically surpassed, can still generate
        new ideas and illuminate our work from a different perspective. Though it
        is infeasible to read all research published on a large topic, looking up
        older papers can be surprisingly rewarding when rediscovering a "gem"at the
        end of a long citation chain, aided by digital collections and perpetually
        helpful librarians. Proper literature study reduces unnecessary repetition
        and allows research to be more insightful and impactful by truly standing
        on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/)
        as dataset MSV000087993.
      authors:
      - name: Neely B.A.
      - name: Palmblad M.
      citationCount: 1
      date: '2021-10-01T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics
        Experiments in the Light of Proteomics'
    note: null
    pmcid: PMC8491155
    pmid: '34523928'
    type:
    - Review
    version: '2.0'
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version:
  - '1.0'
  - '2.0'
- accessibility: Open access
  additionDate: '2025-04-16T08:53:57.270825Z'
  biotoolsCURIE: biotools:openvre
  biotoolsID: openvre
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: laia.codo@bsc.es
    fundrefid: 10.13039/501100006433
    gridid: grid.10097.3f
    name: Laia Codó
    note: Senior Researcher at Barcelona Supercomputing Center. Lead of Trusted Research
      Environments and Cloud Computing at INB Lab.
    orcidid: https://orcid.org/0000-0002-6797-8746
    rorid: 05sd8tv96
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.bsc.es/codo-laia
  - email: gelpi@ub.edu
    fundrefid: 10.13039/501100005774
    gridid: grid.5841.8
    name: Josep Lluís Gelpí
    note: Professor at University of Barcelona and Team Leader at BSC's INB Laboratory
    orcidid: http://orcid.org/0000-0002-0566-7723
    rorid: 021018s57
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://webgrec.ub.edu/webpages/000011/ang/gelpi.ub.edu.html
  description: The Open Virtual Research Environment is a general purpose analysis
    platform that can be tailored for domain specific analyses.
  documentation:
  - note: Getting Started Guide
    type:
    - Quick start guide
    url: http://vre.multiscalegenomics.eu/help/starting.php
  download:
  - note: null
    type: Source code
    url: https://github.com/inab/openVRE
    version: '1.0'
  editPermission:
    authors:
    - gelpi@ub.edu
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Service management
      uri: http://edamontology.org/operation_3760
    output: []
  homepage: https://github.com/inab/openVRE/wiki
  homepage_status: 0
  language:
  - PHP
  - Python
  - JavaScript
  lastUpdate: '2025-04-16T08:53:57.280528Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: openVRE
  operatingSystem:
  - Linux
  otherID: []
  owner: gelpi@ub.edu
  publication: []
  relation:
  - biotoolsID: mugvre
    type: isNewVersionOf
  toolType:
  - Bioinformatics portal
  - Workbench
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2019-05-27T16:33:42Z'
  biotoolsCURIE: biotools:PinMol
  biotoolsID: PinMol
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: iecatrina@gmail.com
    fundrefid: null
    gridid: null
    name: Irina E. Catrina
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Application for designing molecular beacons for live cell imaging of
    endogenous mRNAs.
  documentation:
  - note: Tutorial material
    type:
    - Training material
    url: https://bratulab.wordpress.com/tutorial-pinmol-mac/
  download:
  - note: null
    type: Source code
    url: https://github.com/icatrina/PinMol_Win/releases/tag/v1.0-beta
    version: beta 1.0
  - note: null
    type: Source code
    url: https://github.com/icatrina/PinMol_Mac/releases/tag/v1.0-beta
    version: beta 1.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: RNA secondary structure alignment
      uri: http://edamontology.org/operation_0502
    - term: Nucleic acid folding analysis
      uri: http://edamontology.org/operation_0279
    output: []
  homepage: https://bratulab.wordpress.com/software/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-25T13:45:28.770486Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: PinMol
  operatingSystem:
  - Windows
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1261/rna.069542.118
    metadata:
      abstract: Molecular beacons are nucleic acid oligomers labeled with a fluorophore
        and a quencher that fold in a hairpin-shaped structure, which fluoresce only
        when bound to their target RNA. They are used for the visualization of endogenous
        mRNAs in live cells. Here, we report a Python program (PinMol) that designs
        molecular beacons best suited for live cell imaging by using structural information
        from secondary structures of the target RNA, predicted via energy minimization
        approaches. PinMol takes into account the accessibility of the targeted regions,
        as well as the inter- and intramolecular interactions of each selected probe.
        To demonstrate its applicability, we synthesized an oskar mRNA-specific molecular
        beacon (osk1236), which is selected by PinMol to target a more accessible
        region than a manually designed oskar-specific molecular beacon (osk2216).
        We previously demonstrated osk2216 to be efficient in detecting oskar mRNA
        in in vivo experiments. Here, we show that osk1236 outperformed osk2216 in
        live cell imaging experiments.
      authors:
      - name: Bayer L.V.
      - name: Omar O.S.
      - name: Bratu D.P.
      - name: Catrina I.E.
      citationCount: 6
      date: '2019-03-01T00:00:00Z'
      journal: RNA
      title: 'Pinmol: Python application for designing molecular beacons for live
        cell imaging of endogenous mRNAs'
    note: null
    pmcid: PMC6380279
    pmid: '30573696'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  validated: 1
  version:
  - beta 1.0
- accessibility: Open access
  additionDate: '2016-05-17T10:17:55Z'
  biotoolsCURIE: biotools:proteoformer
  biotoolsID: proteoformer
  collectionID:
  - BIG N2N
  - Proteomics
  - BioBix
  - UGent
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: Steven.Verbruggen@UGent.be
    fundrefid: null
    gridid: null
    name: Steven Verbruggen
    note: Main developer of the 2.0 version
    orcidid: https://orcid.org/0000-0001-9441-9539
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: null
  - email: Gerben.Menschaert@ugent.be
    fundrefid: null
    gridid: null
    name: Gerben Menschaert
    note: PI of this project
    orcidid: https://orcid.org/0000-0002-7575-2085
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jeroen Crappé
    note: Main developer of the 1.0 version
    orcidid: https://orcid.org/0000-0003-1677-9533
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Elvis Ndah
    note: Main developer of the 1.0 version
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sandra Steyaert
    note: Contributor to the 1.0 version
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Alexander Koch
    note: Contributor to the 1.0 version
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ghent University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://www.ugent.be/en
  - email: null
    fundrefid: null
    gridid: null
    name: BioBix
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: http://www.biobix.be/
  description: Proteogenomic pipeline integrating ribosome profiling (RIBO-seq) data
    in the search for new proteoforms in proteomic validation data. The pipeline does
    a genome-wide construction of candidate translation products based on ribosome
    occupancy.
  documentation:
  - note: Full elaborate documentation on usage and installation with lots of examples.
      Main documentation source.
    type:
    - User manual
    url: https://github.com/Biobix/proteoformer/blob/master/README.md
  - note: GPU 3.0 license
    type:
    - Terms of use
    url: https://github.com/Biobix/proteoformer/blob/master/LICENSE
  download:
  - note: GitHub repo
    type: Source code
    url: https://github.com/Biobix/proteoformer
    version: '2.0'
  - note: Galaxy wrapper files
    type: Tool wrapper (Galaxy)
    url: https://github.com/Biobix/proteoformer/tree/master/Galaxy%20files
    version: '1.0'
  editPermission:
    authors:
    - proteomics.bio.tools
    - StevenVerbruggen
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: perl mapping.pl --help
    input:
    - data:
        term: RNA sequence (raw)
        uri: http://edamontology.org/data_3496
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    - term: RNA-seq read count analysis
      uri: http://edamontology.org/operation_3563
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Nucleic acid density plotting
      uri: http://edamontology.org/operation_2284
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    - term: Genome alignment
      uri: http://edamontology.org/operation_3182
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: SNP annotation
      uri: http://edamontology.org/operation_3661
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: SQLite format
        uri: http://edamontology.org/format_3621
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Biobix/proteoformer
  homepage_status: 0
  language:
  - R
  - Perl
  - SQL
  - Python
  lastUpdate: '2024-11-24T21:08:45.743010Z'
  license: GPL-3.0
  link:
  - note: GitHub tool repo (PROTEOFORMER version 2.0)
    type:
    - Repository
    url: https://github.com/Biobix/proteoformer
  - note: Galaxy service of PROTEOFORMER version 1.0 (the Galaxy service of PROTEOFORMER
      version 2.0 is under way)
    type:
    - Galaxy service
    url: http://galaxy.ugent.be/
  - note: Explanation of the tool on the lab's website
    type:
    - Other
    url: http://www.biobix.be/research/downloads/proteoformer/
  maturity: Mature
  name: PROTEOFORMER
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: Katrijn.Vannerum@ugent.be
  publication:
  - doi: 10.1093/nar/gku1283
    metadata:
      abstract: An increasing amount of studies integrate mRNA sequencing data into
        MS-based proteomics to complement the translation product search space. However,
        several factors, including extensive regulation of mRNA translation and the
        need for threeor six-frame-translation, impede the use of mRNAseq data for
        the construction of a protein sequence search database.With that inmind, we
        developed the PROTEOFORMER tool that automatically processes data of the recently
        developed ribosome profiling method (sequencing of ribosome-protected mRNA
        fragments), resulting in genome-wide visualization of ribosome occupancy.
        Our tool also includes a translation initiation site calling algorithm allowing
        the delineation of the open reading frames (ORFs) of all translation products.
        A complete protein synthesisbased sequence database can thus be compiled for
        mass spectrometry-based identification. This approach increases the overall
        protein identification rates with 3% and 11% (improved and new identifications)
        for human and mouse, respectively, and enables proteome-wide detection of
        5'-extended proteoforms, upstream ORF translation and near-cognate translation
        start sites. The PROTEOFORMER tool is available as a stand-alone pipeline
        and has been implemented in the galaxy framework for ease of use.
      authors:
      - name: Crappe J.
      - name: Ndah E.
      - name: Koch A.
      - name: Steyaert S.
      - name: Gawron D.
      - name: De Keulenaer S.
      - name: De Meester E.
      - name: De Meyer T.
      - name: Van Criekinge W.
      - name: Van Damme P.
      - name: Menschaert G.
      citationCount: 111
      date: '2015-03-11T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'PROTEOFORMER: Deep proteome coverage through ribosome profiling and
        MS integration'
    note: null
    pmcid: PMC4357689
    pmid: '25510491'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1074/mcp.ra118.001218
    metadata:
      abstract: PROTEOFORMER is a pipeline that enables the automated processing of
        data derived from ribosome profiling (RIBO-seq, i.e. The sequencing of ribosome-protected
        mRNA fragments). As such, genome-wide ribosome occupancies lead to the delineation
        of data-specific translation product candidates and these can improve the
        mass spectrometry-based identification. Since its first publication, different
        upgrades, new features and extensions have been added to the PROTEOFORMER
        pipeline. Some of the most important upgrades include P-site offset calculation
        during mapping, comprehensive data preexploration, the introduction of two
        alternative proteoform calling strategies and extended pipeline output features.
        These novelties are illustrated by analyzing ribosome profiling data of human
        HCT116 and Jurkat data. The different proteoform calling strategies are used
        alongside one another and in the end combined together with reference sequences
        from UniProt. Matching mass spectrometry data are searched against this extended
        search space with MaxQuant. Overall, besides annotated proteoforms, this pipeline
        leads to the identification and validation of different categories of new
        proteoforms, including translation products of up- and downstream open reading
        frames, 5' and 3' extended and truncated proteoforms, single amino acid variants,
        splice variants and translation products of so-called noncoding regions. Further,
        proof-of-concept is reported for the improvement of spectrum matching by including
        Prosit, a deep neural network strategy that adds extra fragmentation spectrum
        intensity features to the analysis. In the light of ribosome profiling-driven
        proteogenomics, it is shown that this allows validating the spectrum matches
        of newly identified proteoforms with elevated stringency. These updates and
        novel conclusions provide new insights and lessons for the ribosome profiling-based
        proteogenomic research field.
      authors:
      - name: Verbruggen S.
      - name: Ndah E.
      - name: Van Criekinge W.
      - name: Gessulat S.
      - name: Kuster B.
      - name: Wilhelm M.
      - name: Van Damme P.
      - name: Menschaert G.
      citationCount: 36
      date: '2019-01-01T00:00:00Z'
      journal: Molecular and Cellular Proteomics
      title: 'PROTEOFORMER 2.0: Further developments in the ribosome profiling-assisted
        proteogenomic hunt for new proteoforms'
    note: null
    pmcid: PMC6692777
    pmid: '31040227'
    type:
    - Primary
    version: '2.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Protein variants
    uri: http://edamontology.org/topic_3120
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 1
  version:
  - '1.0'
  - '2.0'
- accessibility: Open access
  additionDate: '2019-07-06T07:28:17Z'
  biotoolsCURIE: biotools:iS-CellR
  biotoolsID: iS-CellR
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: mitul.patel@immunocore.com
    fundrefid: null
    gridid: null
    name: Mitulkumar V. Patel
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: iS-CellR (Interactive platform for Single-cell RNAseq) is a web-based
    Shiny application designed to provide a comprehensive analysis of single-cell
    RNA sequencing data.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/immcore/iS-CellR/blob/master/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/immcore/iS-CellR/releases/tag/v1.1
    version: '1.1'
  - note: null
    type: Source code
    url: https://github.com/immcore/iS-CellR/releases/tag/v1.0
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/immcore/iS-CellR
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-24T21:07:42.254501Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/immcore/iS-CellR/issues
  maturity: Mature
  name: iS-CellR
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1093/bioinformatics/bty517
    metadata:
      abstract: Interactive platform for single-cell RNA-sequencing (iS-CellR) is
        a web-based Shiny application that is designed to provide user-friendly, comprehensive
        analysis of single-cell RNA sequencing data. iS-CellR has the capability to
        run on any modern web browser and provides an accessible graphical user interface
        that enables the user to perform complex single-cell RNA-sequencing analysis
        without requiring programming skills.
      authors:
      - name: Patel M.V.
      citationCount: 15
      date: '2018-12-15T00:00:00Z'
      journal: Bioinformatics
      title: 'iS-CellR: A user-friendly tool for analyzing and visualizing single-cell
        RNA sequencing data'
    note: null
    pmcid: PMC6289135
    pmid: '29982379'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: RNA
    uri: http://edamontology.org/topic_0099
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-07-06T06:25:02Z'
  biotoolsCURIE: biotools:Adjutant
  biotoolsID: Adjutant
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: acrisan@cs.ubc.ca
    fundrefid: null
    gridid: null
    name: Anamaria Crisan
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: R-based tool to support topic discovery for systematic and literature
    reviews.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/amcrisan/Adjutant/blob/master/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/amcrisan/Adjutant/releases
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Text mining
      uri: http://edamontology.org/operation_0306
    output: []
  homepage: https://github.com/amcrisan/Adjutant
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-24T21:07:34.125543Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/amcrisan/Adjutant/issues
  maturity: Mature
  name: Adjutant
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1093/bioinformatics/bty722
    metadata:
      abstract: Adjutant is an open-source, interactive and R-based application to
        support mining PubMed for literature reviews. Given a PubMed-compatible search
        query, Adjutant downloads the relevant articles and allows the user to perform
        an unsupervised clustering analysis to identify data-driven topic clusters.
        Following clustering, users can also sample documents using different strategies
        to obtain a more manageable dataset for further analysis. Adjutant makes explicit
        trade-offs between speed and accuracy, which are modifiable by the user, such
        that a complete analysis of several thousand documents can take a few minutes.
        All analytic datasets generated by Adjutant are saved, allowing users to easily
        conduct other downstream analyses that Adjutant does not explicitly support.
      authors:
      - name: Crisan A.
      - name: Munzner T.
      - name: Gardy J.L.
      citationCount: 13
      date: '2019-03-15T00:00:00Z'
      journal: Bioinformatics
      title: 'Adjutant: An R-based tool to support topic discovery for systematic
        and literature reviews'
    note: null
    pmcid: null
    pmid: '30875428'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2017-03-24T09:34:10Z'
  biotoolsCURIE: biotools:dnatools
  biotoolsID: dnatools
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: pongor.sandor@itk.ppke.hu
    fundrefid: null
    gridid: null
    name: Sándor Pongor
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Includes predicting DNA curvature; plotting physicochemical, statistical,
    or locally computed paramaters along DNA sequences; producing a 3-D model of a
    DNA sequence; searching an intron database.
  documentation:
  - note: bend.it® Server
    type:
    - General
    url: http://pongor.itk.ppke.hu/dna/bend_it.html#/bendit_intro
  - note: plot.it® Server
    type:
    - General
    url: http://pongor.itk.ppke.hu/dna/plot_it.html#/plotit_intro
  - note: null
    type:
    - General
    url: http://pongor.itk.ppke.hu/dna/model_it.html#/modelit_intro
  download:
  - note: Bend.it® Standalone version
    type: Software package
    url: https://github.com/r78v10a07/bendit/archive/1.0.tar.gz
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
    - term: Splice site prediction
      uri: http://edamontology.org/operation_0433
    - term: Splicing model analysis
      uri: http://edamontology.org/operation_2499
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output: []
  homepage: http://pongor.itk.ppke.hu/?q=bioinfoservices
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T21:03:59.382352Z'
  license: Unlicense
  link:
  - note: 'plot.it® Server: The Form'
    type:
    - Service
    url: http://pongor.itk.ppke.hu/dna/plot_it.html#/plotit_form
  - note: bend.it® Server
    type:
    - Service
    url: http://pongor.itk.ppke.hu/dna/bend_it.html#/bendit_form
  - note: model.it® Server
    type:
    - Service
    url: http://pongor.itk.ppke.hu/dna/model_it.html#/modelit_form
  maturity: Mature
  name: DNAtools
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkg559
    metadata:
      abstract: The WWW servers at http://www.icgeb.trieste.it/dna/ are dedicated
        to the analysis of user-submitted DNA sequences; plot.it creates parametric
        plots of 45 physicochemical, as well as statistical, parameters; bend.it calculates
        DNA curvature according to various methods. Both programs provide 1D as well
        as 2D plots that allow localisation of peculiar segments within the query.
        The server model.it creates 3D models of canonical or bent DNA starting from
        sequence data and presents the results in the form of a standard PDB file,
        directly viewable on the user's PC using any molecule manipulation program.
        The recently established introns server allows statistical evaluation of introns
        in various taxonomic groups and the comparison of taxonomic groups in terms
        of length, base composition, intron type etc. The options include the analysis
        of splice sites and a probability test for exon-shuffling.
      authors:
      - name: Vlahovicek K.
      - name: Kajan L.
      - name: Pongor S.
      citationCount: 116
      date: '2003-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'DNA analysis servers: Plot.it, bend.it, model.it and IS'
    note: null
    pmcid: PMC168966
    pmid: '12824394'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-01-24T12:37:12Z'
  biotoolsCURIE: biotools:Isodyn
  biotoolsID: Isodyn
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: '“C++”-program simulating the dynamics of metabolites and their isotopic
    isomers in the central metabolic network using a corresponding kinetic model.
    Supports the final step of 13C assisted the fluxomic analysis: evaluation of metabolic
    fluxes consistent with a given mass isotopomer distribution. The previous steps
    are supported by Ramid, Midcor, Isoform.'
  documentation:
  - note: Usage instruction and example
    type:
    - General
    url: https://github.com/seliv55/isodyn
  download:
  - note: null
    type: Downloads page
    url: https://github.com/seliv55/isodyn
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: ./isodyn.out $fiso $fcon $inpar $oudir $fstat $fcmpr $manfi $FNCKAS
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
    note: 'fiso="SW620-Glucose"    # input data: file indicating 13C labeling of metabolites

      fcon=xglc               # input data: file with measured concentrations

      inpar="glc/1"           # input data: initial set of parameters to start

      oudir="glc/"            # output directory

      fstat="glc/statfl"      # path to write the results of fitting: mean and confidence
      intervals

      fcmpr="glc/statfl"      # results of fitting for the conditions used for comparison.

      manfi=77                # number of files to be saved during fitting

      FNCKAS     # various options for the fitting'
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  homepage: https://github.com/seliv55/isodyn
  homepage_status: 0
  language:
  - R
  lastUpdate: '2024-11-24T21:00:18.465360Z'
  license: Freeware
  link:
  - note: Code and example
    type:
    - Repository
    url: https://github.com/seliv55/isodyn
  maturity: null
  name: Isodyn
  operatingSystem:
  - Linux
  otherID: []
  owner: vitaly
  publication:
  - doi: 10.1007/978-1-0716-0159-4_12
    metadata:
      abstract: 'Stable isotope-resolved metabolomics (SIRM), based on the analysis
        of biological samples from living cells incubated with artificial isotope
        enriched substrates, enables mapping the rates of biochemical reactions (metabolic
        fluxes). We developed software supporting a workflow of analysis of SIRM data
        obtained with mass spectrometry (MS). The evaluation of fluxes starting from
        raw MS recordings requires at least three steps of computer support: first,
        extraction of mass spectra of metabolites of interest, then correction of
        the spectra for natural isotope abundance, and finally, evaluation of fluxes
        by simulation of the corrected spectra using a corresponding mathematical
        model. A kinetic model based on ordinary differential equations (ODEs) for
        isotopomers of metabolites of the corresponding biochemical network supports
        the final part of the analysis, which provides a dynamic flux map.'
      authors:
      - name: Selivanov V.A.
      - name: Marin S.
      - name: Tarrago-Celada J.
      - name: Lane A.N.
      - name: Higashi R.M.
      - name: Fan T.W.-M.
      - name: de Atauri P.
      - name: Cascante M.
      citationCount: 5
      date: '2020-01-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: Software supporting a workflow of quantitative dynamic flux maps estimation
        in central metabolism from SIRM experimental data
    note: null
    pmcid: null
    pmid: '31893378'
    type:
    - Method
    version: null
  - doi: 10.1093/bioinformatics/bth412
    metadata:
      abstract: 'Motivation: Analysis of the conversion of 13C glucose within the
        metabolic network allows the evaluation of the biochemical fluxes in interconnecting
        metabolic pathways. Such analyses require solving hundreds of equations with
        respect to individual isotopomer concentrations, and this assumes applying
        special software even for constructing the equations. The algorithm, proposed
        by others could be improved. Method: A C-code linked to the program written
        in Mathematica (Wolfram Research Inc.), constructs and solves differential
        equations for all isotopomer concentrations, using the general enzyme characteristics
        (Km, equilibrium constant, etc.). This code uses innovative algorithm of determination
        for the isotopomers-products, thus essentially decreasing the computation
        time. Feasible metabolic fluxes are provided by the parameters of enzyme kinetics
        found from the data fitting. Results: The software effectively evaluates metabolic
        fluxes based on the measured isotopomer distribution, as was illustrated by
        the analysis of glycolysis and pentose phosphate cycle. The mechanism of transketolase
        and transaldolase catalysis was shown to induce a specific kind of isotopomer
        re-distribution, which, despite the significance of its effect, usually is
        not taken into account. © Oxford University Press 2004; all rights reserved.'
      authors:
      - name: Selivanov V.A.
      - name: Puigjaner J.
      - name: Sillero A.
      - name: Centelles J.J.
      - name: Ramos-Montoya A.
      - name: Lee P.W.-N.
      - name: Cascante M.
      citationCount: 35
      date: '2004-12-12T00:00:00Z'
      journal: Bioinformatics
      title: An optimized algorithm for flux estimation from isotopomer distribution
        in glucose metabolites
    note: null
    pmcid: null
    pmid: '15256408'
    type:
    - Method
    version: null
  - doi: 10.1093/bioinformatics/bti573
    metadata:
      abstract: 'Motivation: Addition of labeled substrates and the measurement of
        the subsequent distribution of the labels in isotopomers in reaction networks
        provide a unique method for assessing metabolic fluxes in whole cells. However,
        owing to insufficiency of information, attempts to quantify the fluxes often
        yield multiple possible sets of solutions that are consistent with a given
        experimental pattern of isotopomers. In the study of the pentose phosphate
        pathways, the need to consider isotope exchange reactions of transketolase
        (TK) and transaldolase (TA) (which in past analyses have often been ignored)
        magnifies this problem; but accounting for the interrelation between the fluxes
        known from biochemical studies and kinetic modeling solves it. The mathematical
        relationships between kinetic and equilibrium constants restrict the domain
        of estimated fluxes to the ones compatible not only with a given set of experimental
        data, but also with other biochemical information. Method: We present software
        that integrates kinetic modeling with isotopomer distribution analysis. It
        solves the ordinary differential equations for total concentrations (accounting
        for the kinetic mechanisms) as well as for all isotopomers in glycolysis and
        the pentose phosphate pathway (PPP). In the PPP the fluxes created in the
        TK and TA reactions are expressed through unitary rate constants. The algorithms
        that account for all the kinetic and equilbrium constant constraints are integrated
        with the previously developed algorithms, which have been further optimized.
        The most time-consuming calculations were programmed directly in assembly
        language; this gave an order of magnitude decrease in the computation time,
        thus allowing analysis of more complex systems. The software was developed
        as C-code linked to a program written in Mathematica (Wolfram Research, Champaign,
        IL), and also as a C++ program independent from Mathematica. Results: Implementing
        constraints imposed by kinetic and equilibrium constants in the isotopomer
        distribution analysis in the data from the cancer cells eliminated estimates
        of fluxes that were inconsistent with the kinetic mechanisms of TK and TA.
        Fluxes measured experimentally in cells can be used to estimate better the
        kinetics of TK and TA as they operate in situ. Thus, our approach of integrating
        various methods for in situ flux analysis opens up the possibility of designing
        new types of experiments to probe metabolic interrelationships, including
        the incorporation of additional biochemical information. © The Author 2005.
        Published by Oxford University Press. All rights reserved.'
      authors:
      - name: Selivanov V.A.
      - name: Meshalkina L.E.
      - name: Solovjeva O.N.
      - name: Kuchel P.W.
      - name: Ramos-Montoya A.
      - name: Kochetov G.A.
      - name: Lee P.W.N.
      - name: Cascante M.
      citationCount: 30
      date: '2005-09-01T00:00:00Z'
      journal: Bioinformatics
      title: 'Rapid simulation and analysis of isotopomer distributions using constraints
        based on enzyme mechanisms: An example from HT29 cancer cells'
    note: null
    pmcid: null
    pmid: '16002431'
    type:
    - Method
    version: null
  - doi: 10.1093/bioinformatics/btl484
    metadata:
      abstract: 'Motivation: Metabolic flux analysis of biochemical reaction networks
        using isotope tracers requires software tools that can analyze the dynamics
        of isotopic isomer (isotopomer) accumulation in metabolites and reveal the
        underlying kinetic mechanisms of metabolism regulation. Since existing tools
        are restricted by the isotopic steady state and remain disconnected from the
        underlying kinetic mechanisms, we have recently developed a novel approach
        for the analysis of tracer-based metabolomic data that meets these requirements.
        The present contribution describes the last step of this development: implementation
        of (i) the algorithms for the determination of the kinetic parameters and
        respective metabolic fluxes consistent with the experimental data and (ii)
        statistical analysis of both fluxes and parameters, thereby lending it a practical
        application. Results: The C++ applications package for dynamic isotopomer
        distribution data analysis was supplemented by (i) five distinct methods for
        resolving a large system of differential equations; (ii) the ''simulated annealing''
        algorithm adopted to estimate the set of parameters and metabolic fluxes,
        which corresponds to the global minimum of the difference between the computed
        and measured isotopomer distributions; and (iii) the algorithms for statistical
        analysis of the estimated parameters and fluxes, which use the covariance
        matrix evaluation, as well as Monte Carlo simulations. An example of using
        this tool for the analysis of 13C distribution in the metabolites of glucose
        degradation pathways has demonstrated the evaluation of optimal set of parameters
        and fluxes consistent with the experimental pattern, their range and statistical
        significance, and also the advantages of using dynamic rather than the usual
        steady-state method of analysis. © 2006 Oxford University Press.'
      authors:
      - name: Selivanov V.A.
      - name: Marin S.
      - name: Lee P.W.N.
      - name: Cascante M.
      citationCount: 31
      date: '2006-11-15T00:00:00Z'
      journal: Bioinformatics
      title: 'Software for dynamic analysis of tracer-based metabolomic data: Estimation
        of metabolic fluxes and their statistical analysis'
    note: null
    pmcid: null
    pmid: '17000750'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Fluxomics
    uri: http://edamontology.org/topic_3955
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2020-01-20T10:07:47Z'
  biotoolsCURIE: biotools:raiss
  biotoolsID: raiss
  collectionID:
  - Institut Pasteur
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: hugues.aschard@pasteur.fr
    fundrefid: null
    gridid: null
    name: Hugues Aschard
    note: null
    orcidid: http://orcid.org/0000-0002-7554-6783
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://research.pasteur.fr/fr/member/hugues-aschard/
  - email: hanna.julienne@pasteur.fr
    fundrefid: null
    gridid: null
    name: Hanna Julienne
    note: null
    orcidid: https://orcid.org/0000-0001-8214-9412
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://research.pasteur.fr/fr/member/hanna-julienne/
  - email: null
    fundrefid: null
    gridid: null
    name: Bogdan Pasaniuc
    note: null
    orcidid: https://orcid.org/0000-0002-0227-2056
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Huwenbo Shi
    note: null
    orcidid: https://orcid.org/0000-0001-9886-877X
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: software package enabling the imputation of SNP summary statistics
    from the neighboring SNPs by taking advantage of the Linkage desiquilibrium.
  documentation:
  - note: null
    type:
    - General
    url: http://statistical-genetics.pages.pasteur.fr/raiss/
  download:
  - note: null
    type: Container file
    url: https://biocontainers.pro/#/tools/raiss
    version: 1.0, 2.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: null
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: http://statistical-genetics.pages.pasteur.fr/raiss/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T20:59:22.136271Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.pasteur.fr/statistical-genetics/raiss
  - note: null
    type:
    - Issue tracker
    url: https://gitlab.pasteur.fr/statistical-genetics/raiss/issues
  maturity: Mature
  name: RAISS
  operatingSystem:
  - Linux
  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1093/bioinformatics/btz466
    metadata:
      abstract: 'Multi-trait analyses using public summary statistics from genome-wide
        association studies (GWASs) are becoming increasingly popular. A constraint
        of multi-trait methods is that they require complete summary data for all
        traits. Although methods for the imputation of summary statistics exist, they
        lack precision for genetic variants with small effect size. This is benign
        for univariate analyses where only variants with large effect size are selected
        a posteriori. However, it can lead to strong p-value inflation in multi-trait
        testing. Here we present a new approach that improve the existing imputation
        methods and reach a precision suitable for multi-trait analyses. Results:
        We fine-tuned parameters to obtain a very high accuracy imputation from summary
        statistics. We demonstrate this accuracy for variants of all effect sizes
        on real data of 28 GWAS. We implemented the resulting methodology in a python
        package specially designed to efficiently impute multiple GWAS in parallel.'
      authors:
      - name: Julienne H.
      - name: Shi H.
      - name: Pasaniuc B.
      - name: Aschard H.
      citationCount: 14
      date: '2019-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'RAISS: Robust and accurate imputation from summary statistics'
    note: null
    pmcid: PMC6853677
    pmid: '31173064'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 1
  version:
  - 1.0, 2.0
- accessibility: Open access
  additionDate: '2016-06-30T09:32:44Z'
  biotoolsCURIE: biotools:predictsnp2
  biotoolsID: predictsnp2
  collectionID:
  - Czech Republic
  - Rare Disease
  - ELIXIR-CZ
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: jaroslav.bendl@gmail.com
    fundrefid: null
    gridid: null
    name: Jaroslav Bendl
    note: null
    orcidid: https://orcid.org/0000-0001-9989-2720
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: stourac.jan@gmail.com
    fundrefid: null
    gridid: null
    name: Jan Stourac
    note: null
    orcidid: https://orcid.org/0000-0003-3139-3700
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Support
    url: null
  - email: xmusil46@stud.fit.vutbr.cz
    fundrefid: null
    gridid: null
    name: Milos Musil
    note: null
    orcidid: https://orcid.org/0000-0001-9373-7930
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: brezovsky@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Jan Brezovsky
    note: null
    orcidid: https://orcid.org/0000-0001-9677-5078
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: 1441@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Jiri Damborsky
    note: null
    orcidid: https://orcid.org/0000-0002-7848-8216
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Eric D. Wieben
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: zendulka@fit.vut.cz
    fundrefid: null
    gridid: null
    name: Jaroslav Zendulka
    note: null
    orcidid: https://orcid.org/0000-0001-8718-7493
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: 99207@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Antonin Pavelka
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Loschmidt Laboratories
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://loschmidt.chemi.muni.cz/peg/
  - email: null
    fundrefid: null
    gridid: null
    name: Masaryk University, Brno, Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.muni.cz/
  - email: null
    fundrefid: null
    gridid: null
    name: International Centre for Clinical Research, Brno, Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.fnusa-icrc.org/en/
  - email: null
    fundrefid: null
    gridid: null
    name: Brno University of Technology, Brno, Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.vutbr.cz/
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-CZ
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://www.elixir-czech.cz/
  - email: predictsnp@sci.muni.cz
    fundrefid: null
    gridid: null
    name: PredictSNP team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: European Regional Development Fund
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: European Social Fund
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Grant Agency of the Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ministry of Education of the Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Brno University of Technology
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  description: A consensus classifier that combines five of the top performing tools
    (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect
    of SNPs within the human genome. The obtained results are provided together with
    annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg,
    UCSC and Ensembl databases.
  documentation:
  - note: null
    type:
    - User manual
    url: https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdf
  download:
  - note: null
    type: Downloads page
    url: https://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: GVF
        uri: http://edamontology.org/format_3019
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: VCF file containing scores and PDF file containing scores and database links
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://loschmidt.chemi.muni.cz/predictsnp2
  homepage_status: 0
  language:
  - JavaScript
  - Java
  lastUpdate: '2024-11-24T20:23:08.475881Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: PredictSNP2
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Loschmidt Laboratories
  publication:
  - doi: 10.1371/journal.pcbi.1004962
    metadata:
      abstract: 'An important message taken from human genome sequencing projects
        is that the human population exhibits approximately 99.9% genetic similarity.
        Variations in the remaining parts of the genome determine our identity, trace
        our history and reveal our heritage. The precise delineation of phenotypically
        causal variants plays a key role in providing accurate personalized diagnosis,
        prognosis, and treatment of inherited diseases. Several computational methods
        for achieving such delineation have been reported recently. However, their
        ability to pinpoint potentially deleterious variants is limited by the fact
        that their mechanisms of prediction do not account for the existence of different
        categories of variants. Consequently, their output is biased towards the variant
        categories that are most strongly represented in the variant databases. Moreover,
        most such methods provide numeric scores but not binary predictions of the
        deleteriousness of variants or confidence scores that would be more easily
        understood by users. We have constructed three datasets covering different
        types of disease-related variants, which were divided across five categories:
        (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense
        variants. These datasets were used to develop category-optimal decision thresholds
        and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM,
        FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages
        of the category-based approach. The results obtained with the five best-performing
        tools were then combined into a consensus score. Additional comparative analyses
        showed that in the case of missense variations, protein-based predictors perform
        better than DNA sequence-based predictors. A user-friendly web interface was
        developed that provides easy access to the five tools’ predictions, and their
        consensus scores, in a user-understandable format tailored to the specific
        features of different categories of variations. To enable comprehensive evaluation
        of variants, the predictions are complemented with annotations from eight
        databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2.'
      authors:
      - name: Bendl J.
      - name: Musil M.
      - name: Stourac J.
      - name: Zendulka J.
      - name: Damborsky J.
      - name: Brezovsky J.
      citationCount: 143
      date: '2016-05-01T00:00:00Z'
      journal: PLoS Computational Biology
      title: 'PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects
        by Exploiting the Different Characteristics of Variants in Distinct Genomic
        Regions'
    note: null
    pmcid: PMC4880439
    pmid: '27224906'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Web application
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: DNA mutation
    uri: http://edamontology.org/topic_2533
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2018-04-06T08:55:47Z'
  biotoolsCURIE: biotools:caverdock
  biotoolsID: caverdock
  collectionID:
  - CAVER
  - ELIXIR-CZ
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: fila@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Jiri Filipovic
    note: null
    orcidid: https://orcid.org/0000-0002-5703-9673
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: o.vavra@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Ondrej Vavra
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: 408420@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Jan Plhak
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: 222755@mail.muni.cz
    fundrefid: null
    gridid: null
    name: David Bednar
    note: null
    orcidid: https://orcid.org/0000-0002-6803-0340
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: smar96@gmail.com
    fundrefid: null
    gridid: null
    name: Sergio Marques
    note: null
    orcidid: https://orcid.org/0000-0002-6281-7505
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: brezovsky@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Jan Brezovsky
    note: null
    orcidid: https://orcid.org/0000-0001-9677-5078
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: stourac.jan@gmail.com
    fundrefid: null
    gridid: null
    name: Jan Stourac
    note: null
    orcidid: https://orcid.org/0000-0003-3139-3700
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Support
    url: null
  - email: Ludek.Matyska@muni.cz
    fundrefid: null
    gridid: null
    name: Ludek Matyska
    note: null
    orcidid: https://orcid.org/0000-0001-6399-5453
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: 1441@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Jiri Damborsky
    note: null
    orcidid: https://orcid.org/0000-0002-7848-8216
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Loschmidt Laboratories
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://loschmidt.chemi.muni.cz/peg/
  - email: null
    fundrefid: null
    gridid: null
    name: Masaryk University, Brno, Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.muni.cz/
  - email: null
    fundrefid: null
    gridid: null
    name: International Centre for Clinical Research, Brno, Czech Republic
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.fnusa-icrc.org/en/
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-CZ
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://www.elixir-czech.cz/
  - email: caver@caver.cz
    fundrefid: null
    gridid: null
    name: CaverDock team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: European Commission
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Czech Science Foundation
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Brno City Municipality
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
    - Contributor
    url: null
  description: Performs rapid analysis of transport processes in proteins. It models
    the transportation of a ligand from outside environment into the protein active
    or binding site and vice versa. It implements a novel algorithm to produce contiguous
    ligand trajectory and estimation of a binding energy along the pathway. The current
    version uses CAVER for pathway identification and heavily modified Autodock Vina
    as a docking engine.
  documentation:
  - note: version 1.0
    type:
    - User manual
    url: https://www.fi.muni.cz/~xfilipov/caverdock/manual.pdf
  - note: version 1.1
    type:
    - User manual
    url: https://www.fi.muni.cz/~xfilipov/caverdock/manual-1.1.pdf
  download:
  - note: v1.0, Ubuntu 14.04
    type: Binaries
    url: https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-14.04.tar.gz
    version: '1.0'
  - note: v1.0, Ubuntu 16.04
    type: Binaries
    url: https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-16.04.tar.gz
    version: '1.0'
  - note: v1.1, Ubuntu 16.04
    type: Binaries
    url: https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-16.04.tar.xz
    version: '1.1'
  - note: v1.1, Ubuntu 18.04
    type: Binaries
    url: https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-18.04.tar.xz
    version: '1.1'
  editPermission:
    authors:
    - ELIXIR-CZ
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: trajectory of ligand passing through protein tunnel and its energy
    operation:
    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    output:
    - data:
        term: Protein structure report
        uri: http://edamontology.org/data_1537
      format:
      - term: raw
        uri: http://edamontology.org/format_1957
      - term: PDB
        uri: http://edamontology.org/format_1476
  homepage: https://loschmidt.chemi.muni.cz/caverdock/
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2024-11-24T20:23:05.902530Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: CaverDock
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Loschmidt Laboratories
  publication:
  - doi: 10.1093/bioinformatics/btz386
    metadata:
      abstract: 'Motivation: Protein tunnels and channels are key transport pathways
        that allow ligands to pass between proteins'' external and internal environments.
        These functionally important structural features warrant detailed attention.
        It is difficult to study the ligand binding and unbinding processes experimentally,
        while molecular dynamics simulations can be time-consuming and computationally
        demanding. Results: CaverDock is a new software tool for analysing the ligand
        passage through the biomolecules. The method uses the optimized docking algorithm
        of AutoDock Vina for ligand placement docking and implements a parallel heuristic
        algorithm to search the space of possible trajectories. The duration of the
        simulations takes from minutes to a few hours. Here we describe the implementation
        of the method and demonstrate CaverDock''s usability by: (i) comparison of
        the results with other available tools, (ii) determination of the robustness
        with large ensembles of ligands and (iii) the analysis and comparison of the
        ligand trajectories in engineered tunnels. Thorough testing confirms that
        CaverDock is applicable for the fast analysis of ligand binding and unbinding
        in fundamental enzymology and protein engineering. Availability and implementation:
        User guide and binaries for Ubuntu are freely available for non-commercial
        use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation
        is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code
        is available upon request. Supplementary information: Supplementary data are
        available at Bioinformatics online.'
      authors:
      - name: Vavra O.
      - name: Filipovic J.
      - name: Plhak J.
      - name: Bednar D.
      - name: Marques S.M.
      - name: Brezovsky J.
      - name: Stourac J.
      - name: Matyska L.
      - name: Damborsky J.
      citationCount: 55
      date: '2019-12-01T00:00:00Z'
      journal: Bioinformatics
      title: 'CaverDock: A molecular docking-based tool to analyse ligand transport
        through protein tunnels and channels'
    note: null
    pmcid: null
    pmid: '31077297'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1109/tcbb.2019.2907492
    metadata:
      abstract: Here we present a novel method for the analysis of transport processes
        in proteins and its implementation called CaverDock. Our method is based on
        a modified molecular docking algorithm. It iteratively places the ligand along
        the access tunnel in such a way that the ligand movement is contiguous and
        the energy is minimized. The result of CaverDock calculation is a ligand trajectory
        and an energy profile of transport process. CaverDock uses the modified docking
        program Autodock Vina for molecular docking and implements a parallel heuristic
        algorithm for searching the space of possible trajectories. Our method lies
        in between the geometrical approaches and molecular dynamics simulations.
        Contrary to the geometrical methods, it provides an evaluation of chemical
        forces. However, it is far less computationally demanding and easier to set
        up compared to molecular dynamics simulations. CaverDock will find a broad
        use in the fields of computational enzymology, drug design, and protein engineering.
        The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.
      authors:
      - name: Filipovic J.
      - name: Vavra O.
      - name: Plhak J.
      - name: Bednar D.
      - name: Marques S.M.
      - name: Brezovsky J.
      - name: Matyska L.
      - name: Damborsk J.
      citationCount: 26
      date: '2020-09-01T00:00:00Z'
      journal: IEEE/ACM Transactions on Computational Biology and Bioinformatics
      title: 'CaverDock: A Novel Method for the Fast Analysis of Ligand Transport'
    note: null
    pmcid: null
    pmid: '30932844'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version:
  - '1.0'
  - '1.1'
- accessibility: null
  additionDate: '2019-11-22T12:35:23Z'
  biotoolsCURIE: biotools:WHISCY
  biotoolsID: WHISCY
  collectionID:
  - BioExcel
  - WeNMR
  - INSTRUCT
  - EGI
  confidence_flag: null
  cost: null
  credit:
  - email: a.m.j.j.bonvin@uu.nl
    fundrefid: null
    gridid: null
    name: Bonvin Lab
    note: null
    orcidid: http://orcid.org/0000-0001-7369-1322
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    - Maintainer
    - Developer
    - Primary contact
    url: http://www.bonvinlab.org
  - email: null
    fundrefid: null
    gridid: null
    name: Utrecht University
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.uu.nl
  - email: null
    fundrefid: null
    gridid: null
    name: Netherlands Organization for Scientific Research (NWO), VICI grant no. 700.96.442
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: WHISCY is a program to predict protein-protein interfaces. It is primarily
    based on conservation, but it also takes into account structural information.
    A sequence alignment is used to calculate a prediction score for each surface
    residue of your protein.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/haddocking/whiscy
  download:
  - note: null
    type: Downloads page
    url: https://github.com/haddocking/whiscy/releases
    version: '1.0'
  editPermission:
    authors:
    - br.jimenezgarcia@gmail.com
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Netherlands
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://bianca.science.uu.nl/whiscy/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T15:23:01.942171Z'
  license: null
  link: []
  maturity: Mature
  name: WHISCY
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: a.m.j.j.bonvin@uu.nl
  publication:
  - doi: 10.1002/prot.20842
    metadata:
      abstract: Protein-protein interactions play a key role in biological processes.
        Identifying the interacting residues is a first step toward understanding
        these interactions at a structural level. In this study, the interface prediction
        program WHISCY is presented. It combines surface conservation and structural
        information to predict protein-protein interfaces. The accuracy of the predictions
        is more than three times higher than a random prediction. These predictions
        have been combined with another interface prediction program, ProMate [Neuvirth
        et al. J Mol Biol 2004;338:181-199], resulting in an even more accurate predictor.
        The usefulness of the predictions was tested using the data-driven docking
        program HADDOCK [Dominguez et al. J Am Chem Soc 2003;125:1731-1737] in an
        unbound docking experiment, with the goal of generating as many near-native
        structures as possible. Unrefined rigid body docking solutions within 10 Å
        ligand RMSD from the true structure were generated for 22 out of 25 docked
        complexes. For 18 complexes, more than 100 of the 8000 generated models were
        correct. Our results demonstrates the potential of using interface predictions
        to drive protein-protein docking. © 2006 Wiley-Liss, Inc.
      authors:
      - name: De Vries S.J.
      - name: Van Dijk A.D.J.
      - name: Bonvin A.M.J.J.
      citationCount: 125
      date: '2006-05-15T00:00:00Z'
      journal: 'Proteins: Structure, Function and Genetics'
      title: 'WHISCY: What information does surface conservation yield? Application
        to data-driven docking'
    note: null
    pmcid: null
    pmid: '16450362'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-05-25T11:54:30.874289Z'
  biotoolsCURIE: biotools:3d-bioinfo_bioexcel_protein_conformational_ensembles_generation
  biotoolsID: 3d-bioinfo_bioexcel_protein_conformational_ensembles_generation
  collectionID:
  - BioExcel
  - 3D-BioInfo
  - 3D-BioInfo-Protein-Complex
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/genis-bayarri
  - email: katharina.heil@elixir-europe.org
    fundrefid: null
    gridid: null
    name: 3D-BioInfo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://elixir-europe.org/communities/3d-bioinfo
  description: 'This workflow illustrates the process of generating protein conformational
    ensembles from 3D structures and analysing its molecular flexibility, step by
    step, using the BioExcel Building Blocks library (biobb). Workflow included in
    the ELIXIR 3D-Bioinfo Implementation Study: Building on PDBe-KB to chart and characterize
    the conformation landscape of native proteins'
  documentation:
  - note: Read The Docs Workflow Documentation
    type:
    - Other
    url: https://biobb-wf-flexdyn.readthedocs.io/en/latest/?badge=latest
  download:
  - note: null
    type: Source code
    url: https://github.com/bioexcel/biobb_wf_flexdyn
    version: '1.0'
  - note: BioExcel Binder
    type: VM image
    url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_md_setup/master?filepath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Spain
  - Norway
  - France
  - Belgium
  - EMBL
  - Hungary
  - Denmark
  elixirPlatform:
  - Interoperability
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Trajectory visualization
      uri: http://edamontology.org/operation_3890
    - term: Protein property calculation
      uri: http://edamontology.org/operation_0250
    - term: Principal component visualisation
      uri: http://edamontology.org/operation_2939
    output:
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PCAzip
        uri: http://edamontology.org/format_3874
  homepage: https://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:47:40.290064Z'
  license: Apache-2.0
  link:
  - note: Main web site (BioBB workflows)
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation
  - note: Tutorial in HTML
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexdyn
  - note: Tutorial in Read The Docs
    type:
    - Other
    url: https://biobb-wf-flexdyn.readthedocs.io/en/latest/index.html
  - note: Source Code in GitHub
    type:
    - Repository
    url: https://github.com/bioexcel/biobb_wf_flexdyn
  maturity: Emerging
  name: '3D-BioInfo + BioExcel: Protein Conformational Ensembles Generation'
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication:
  - doi: 10.1038/s41597-019-0177-4
    metadata:
      abstract: In the recent years, the improvement of software and hardware performance
        has made biomolecular simulations a mature tool for the study of biological
        processes. Simulation length and the size and complexity of the analyzed systems
        make simulations both complementary and compatible with other bioinformatics
        disciplines. However, the characteristics of the software packages used for
        simulation have prevented the adoption of the technologies accepted in other
        bioinformatics fields like automated deployment systems, workflow orchestration,
        or the use of software containers. We present here a comprehensive exercise
        to bring biomolecular simulations to the “bioinformatics way of working”.
        The exercise has led to the development of the BioExcel Building Blocks (BioBB)
        library. BioBB’s are built as Python wrappers to provide an interoperable
        architecture. BioBB’s have been integrated in a chain of usual software management
        tools to generate data ontologies, documentation, installation packages, software
        containers and ways of integration with workflow managers, that make them
        usable in most computational environments.
      authors:
      - name: Andrio P.
      - name: Hospital A.
      - name: Conejero J.
      - name: Jorda L.
      - name: Del Pino M.
      - name: Codo L.
      - name: Soiland-Reyes S.
      - name: Goble C.
      - name: Lezzi D.
      - name: Badia R.M.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 39
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Data
      title: BioExcel Building Blocks, a software library for interoperable biomolecular
        simulation workflows
    note: BioExcel Building Blocks (BioBB)
    pmcid: PMC6736963
    pmid: '31506435'
    type:
    - Other
    version: null
  - doi: 10.12688/f1000research.20559.1
    metadata:
      abstract: Structural bioinformatics provides the scientific methods and tools
        to analyse, archive, validate, and present the biomolecular structure data
        generated by the structural biology community. It also provides an important
        link with the genomics community, as structural bioinformaticians also use
        the extensive sequence data to predict protein structures and their functional
        sites. A very broad and active community of structural bioinformaticians exists
        across Europe, and 3D-Bioinfo will establish formal platforms to address their
        needs and better integrate their activities and initiatives. Our mission will
        be to strengthen the ties with the structural biology research communities
        in Europe covering life sciences, as well as chemistry and physics and to
        bridge the gap between these researchers in order to fully realize the potential
        of structural bioinformatics. Our Community will also undertake dedicated
        educational, training and outreach efforts to facilitate this, bringing new
        insights and thus facilitating the development of much needed innovative applications
        e.g. for human health, drug and protein design. Our combined efforts will
        be of critical importance to keep the European research efforts competitive
        in this respect. Here we highlight the major European contributions to the
        field of structural bioinformatics, the most pressing challenges remaining
        and how Europe-wide interactions, enabled by ELIXIR and its platforms, will
        help in addressing these challenges and in coordinating structural bioinformatics
        resources across Europe. In particular, we present recent activities and future
        plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics
        and propose means to develop better links across the community. These include
        building new consortia, organising workshops to establish data standards and
        seeking community agreement on benchmark data sets and strategies. We also
        highlight existing and planned collaborations with other ELIXIR Communities
        and other European infrastructures, such as the structural biology community
        supported by Instruct-ERIC, with whom we have synergies and overlapping common
        interests.
      authors:
      - name: Orengo C.
      - name: Velankar S.
      - name: Wodak S.
      - name: Zoete V.
      - name: Bonvin A.M.J.J.
      - name: Elofsson A.
      - name: Feenstra K.A.
      - name: Gerloff D.L.
      - name: Hamelryck T.
      - name: Hancock J.M.
      - name: Helmer-Citterich M.
      - name: Hospital A.
      - name: Orozco M.
      - name: Perrakis A.
      - name: Rarey M.
      - name: Soares C.
      - name: Sussman J.L.
      - name: Thornton J.M.
      - name: Tuffery P.
      - name: Tusnady G.
      - name: Wierenga R.
      - name: Salminen T.
      - name: Schneider B.
      citationCount: 10
      date: '2020-01-01T00:00:00Z'
      journal: F1000Research
      title: A community proposal to integrate structural bioinformatics activities
        in ELIXIR (3D-Bioinfo Community)
    note: 3D-BioInfo, ELIXIR Structural Community
    pmcid: PMC7284151
    pmid: '32566135'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: biobb
    type: uses
  - biotoolsID: imod
    type: uses
  - biotoolsID: flexserv
    type: uses
  - biotoolsID: prody
    type: uses
  - biotoolsID: nglview
    type: uses
  toolType:
  - Workflow
  topic:
  - term: Biomolecular simulation
    uri: http://edamontology.org/topic_3892
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-07-03T10:51:19.368916Z'
  biotoolsCURIE: biotools:suchtree
  biotoolsID: suchtree
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Russell Y. Neches
    note: null
    orcidid: https://orcid.org/0000-0002-2055-8381
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://vort.org
  - email: null
    fundrefid: null
    gridid: null
    name: Camille Scott
    note: null
    orcidid: https://orcid.org/0000-0001-8822-8779
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: http://www.camillescott.org/
  description: A Python library for doing fast, thread-safe computations with phylogenetic
    trees.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/ryneches/SuchTree#readme
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/SuchTree/
    version: '1.0'
  editPermission:
    authors:
    - sbzzz
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: SuchTree.distances_by_name()
    input:
    - data:
        term: Gene tree
        uri: http://edamontology.org/data_3271
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    note: null
    operation:
    - term: Phylogenetic tree distances calculation
      uri: http://edamontology.org/operation_0557
    - term: Phylogenetic tree topology analysis
      uri: http://edamontology.org/operation_0551
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    output:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: NumPy format
        uri: http://edamontology.org/format_4003
  homepage: https://github.com/ryneches/SuchTree
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:45:55.043514Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ryneches/SuchTree
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ryneches/SuchTree/issues
  maturity: Emerging
  name: SuchTree
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ryneches
  publication:
  - doi: 10.21105/joss.00678
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '0.7'
  relation: []
  toolType:
  - Library
  topic:
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-07-26T14:34:25.798022Z'
  biotoolsCURIE: biotools:kojak
  biotoolsID: kojak
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A database search algorithm for solving cross-linked peptide mass spectra.
  documentation:
  - note: null
    type:
    - Quick start guide
    - Installation instructions
    - User manual
    url: https://kojak-ms.systemsbiology.net/docs/index.html
  - note: null
    type:
    - Command-line options
    url: https://kojak-ms.systemsbiology.net/param/index.html
  download:
  - note: null
    type: Downloads page
    url: https://kojak-ms.systemsbiology.net/download.html
    version: 1.0 - 2.0.0
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Proteomics
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://kojak-ms.systemsbiology.net/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-24T14:45:40.796568Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: Kojak
  operatingSystem:
  - Linux
  - Windows
  otherID: []
  owner: mhoopmann
  publication:
  - doi: 10.1021/pr501321h
    metadata:
      abstract: Protein chemical cross-linking and mass spectrometry enable the analysis
        of protein-protein interactions and protein topologies; however, complicated
        cross-linked peptide spectra require specialized algorithms to identify interacting
        sites. The Kojak cross-linking software application is a new, efficient approach
        to identify cross-linked peptides, enabling large-scale analysis of protein-protein
        interactions by chemical cross-linking techniques. The algorithm integrates
        spectral processing and scoring schemes adopted from traditional database
        search algorithms and can identify cross-linked peptides using many different
        chemical cross-linkers with or without heavy isotope labels. Kojak was used
        to analyze both novel and existing data sets and was compared to existing
        cross-linking algorithms. The algorithm provided increased cross-link identifications
        over existing algorithms and, equally importantly, the results in a fraction
        of computational time. The Kojak algorithm is open-source, cross-platform,
        and freely available. This software provides both existing and new cross-linking
        researchers alike an effective way to derive additional cross-link identifications
        from new or existing data sets. For new users, it provides a simple analytical
        resource resulting in more cross-link identifications than other methods.
      authors:
      - name: Hoopmann M.R.
      - name: Zelter A.
      - name: Johnson R.S.
      - name: Riffle M.
      - name: Maccoss M.J.
      - name: Davis T.N.
      - name: Moritz R.L.
      citationCount: 142
      date: '2015-05-01T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'Kojak: Efficient analysis of chemically cross-linked protein complexes'
    note: null
    pmcid: PMC4428575
    pmid: '25812159'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1021/acs.jproteome.2c00670
    metadata:
      abstract: Fragmentation ion spectral analysis of chemically cross-linked proteins
        is an established technology in the proteomics research repertoire for determining
        protein interactions, spatial orientation, and structure. Here we present
        Kojak version 2.0, a major update to the original Kojak algorithm, which was
        developed to identify cross-linked peptides from fragment ion spectra using
        a database search approach. A substantially improved algorithm with updated
        scoring metrics, support for cleavable cross-linkers, and identification of
        cross-links between 15N-labeled homomultimers are among the newest features
        of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic
        Pipeline, enabling access to dozens of additional tools within that suite.
        In particular, the PeptideProphet and iProphet tools for validation of cross-links
        improve the sensitivity and accuracy of correct cross-link identifications
        at user-defined thresholds. These new features improve the versatility of
        the algorithm, enabling its use in a wider range of experimental designs and
        analysis pipelines. Kojak 2.0 remains open-source and multiplatform.
      authors:
      - name: Hoopmann M.R.
      - name: Shteynberg D.D.
      - name: Zelter A.
      - name: Riffle M.
      - name: Lyon A.S.
      - name: Agard D.A.
      - name: Luan Q.
      - name: Nolen B.J.
      - name: MacCoss M.J.
      - name: Davis T.N.
      - name: Moritz R.L.
      citationCount: 4
      date: '2023-02-03T00:00:00Z'
      journal: Journal of Proteome Research
      title: Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak
        2.0, Advanced by Integration into the Trans-Proteomic Pipeline
    note: null
    pmcid: PMC10234491
    pmid: '36629399'
    type:
    - Primary
    version: 2.0.0
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2023-08-29T10:55:17.540852Z'
  biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_macromolecular_coarse-grained_flexibility
  biotoolsID: bioexcel_building_blocks_tutorials_macromolecular_coarse-grained_flexibility
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: null
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: https://orcid.org/0000-0003-0513-0288
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.irbbarcelona.org/es/research/genis-bayarri
  - email: null
    fundrefid: null
    gridid: null
    name: BioExcel CoE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://bioexcel.eu/
  description: This tutorial aims to illustrate the process of generating protein
    conformational ensembles from 3D structures using Coarse-Grained tools from the
    FlexServ server and analysing its molecular flexibility
  documentation:
  - note: Read The Docs workflow documentation
    type:
    - Other
    url: https://biobb-wf-flexserv.readthedocs.io/en/latest/index.html
  download:
  - note: null
    type: Source code
    url: https://github.com/bioexcel/biobb_wf_flexserv
    version: '1.0'
  - note: BioExcel Binder
    type: VM image
    url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_flexserv/main?filepath=biobb_wf_flexserv%2Fnotebooks%2Fbiobb_wf_flexserv.ipynb
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Spain
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Trajectory visualization
      uri: http://edamontology.org/operation_3890
    - term: Protein property calculation
      uri: http://edamontology.org/operation_0250
    - term: Principal component visualisation
      uri: http://edamontology.org/operation_2939
    output:
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: PCAzip
        uri: http://edamontology.org/format_3874
  homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexserv
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:42:53.650928Z'
  license: Apache-2.0
  link:
  - note: Main web site (BioBB Workflows)
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows#macromolecular-coarse-grained-flexibility
  - note: Tutorial in HTML
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexserv
  - note: Tutorial in Read The Docs
    type:
    - Other
    url: https://biobb-wf-flexserv.readthedocs.io/en/latest/index.html
  - note: Source Code in GitHub
    type:
    - Repository
    url: https://github.com/bioexcel/biobb_wf_flexserv
  maturity: Emerging
  name: 'BioExcel Building Blocks tutorials: Macromolecular Coarse-Grained Flexibility'
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication:
  - doi: 10.1038/s41597-019-0177-4
    metadata:
      abstract: In the recent years, the improvement of software and hardware performance
        has made biomolecular simulations a mature tool for the study of biological
        processes. Simulation length and the size and complexity of the analyzed systems
        make simulations both complementary and compatible with other bioinformatics
        disciplines. However, the characteristics of the software packages used for
        simulation have prevented the adoption of the technologies accepted in other
        bioinformatics fields like automated deployment systems, workflow orchestration,
        or the use of software containers. We present here a comprehensive exercise
        to bring biomolecular simulations to the “bioinformatics way of working”.
        The exercise has led to the development of the BioExcel Building Blocks (BioBB)
        library. BioBB’s are built as Python wrappers to provide an interoperable
        architecture. BioBB’s have been integrated in a chain of usual software management
        tools to generate data ontologies, documentation, installation packages, software
        containers and ways of integration with workflow managers, that make them
        usable in most computational environments.
      authors:
      - name: Andrio P.
      - name: Hospital A.
      - name: Conejero J.
      - name: Jorda L.
      - name: Del Pino M.
      - name: Codo L.
      - name: Soiland-Reyes S.
      - name: Goble C.
      - name: Lezzi D.
      - name: Badia R.M.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 39
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Data
      title: BioExcel Building Blocks, a software library for interoperable biomolecular
        simulation workflows
    note: BioExcel Building Blocks (BioBB)
    pmcid: PMC6736963
    pmid: '31506435'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: biobb
    type: uses
  - biotoolsID: flexserv
    type: uses
  - biotoolsID: nglview
    type: uses
  - biotoolsID: pcasuite
    type: uses
  toolType:
  - Workflow
  topic:
  - term: Biomolecular simulation
    uri: http://edamontology.org/topic_3892
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-08-29T13:59:17.320256Z'
  biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_molecular_interaction_potentials
  biotoolsID: bioexcel_building_blocks_tutorials_molecular_interaction_potentials
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: null
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: https://orcid.org/0000-0003-0513-0288
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.irbbarcelona.org/es/research/genis-bayarri
  - email: null
    fundrefid: null
    gridid: null
    name: BioExcel CoE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://bioexcel.eu/
  description: This tutorial aims to illustrate the process of computing classical
    molecular interaction potentials from protein structures step by step, using the
    BioExcel Building Blocks library (biobb)
  documentation:
  - note: Read the Docs workflow documentation
    type:
    - Other
    url: https://biobb-wf-cmip.readthedocs.io/en/latest/index.html
  download:
  - note: null
    type: Source code
    url: https://github.com/bioexcel/biobb_wf_cmip
    version: '1.0'
  - note: BioExcel Binder
    type: VM image
    url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_cmip/main?filepath=biobb_wf_cmip%2Fnotebooks%2Fbiobb_wf_cmip.ipynb
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Spain
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    - term: Structure analysis
      uri: http://edamontology.org/operation_2480
    - term: Protein-protein interaction analysis
      uri: http://edamontology.org/operation_2949
    - term: Residue contact prediction
      uri: http://edamontology.org/operation_0272
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    output:
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmip
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:42:17.344237Z'
  license: Apache-2.0
  link:
  - note: Tutorial in HTML
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmip
  - note: Tutorial in Read The Docs
    type:
    - Other
    url: https://biobb-wf-cmip.readthedocs.io/en/latest/index.html
  - note: Source Code in GitHub
    type:
    - Repository
    url: https://github.com/bioexcel/biobb_wf_cmip
  maturity: Emerging
  name: 'BioExcel Building Blocks tutorials: Molecular Interaction Potentials'
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication:
  - doi: 10.1038/s41597-019-0177-4
    metadata:
      abstract: In the recent years, the improvement of software and hardware performance
        has made biomolecular simulations a mature tool for the study of biological
        processes. Simulation length and the size and complexity of the analyzed systems
        make simulations both complementary and compatible with other bioinformatics
        disciplines. However, the characteristics of the software packages used for
        simulation have prevented the adoption of the technologies accepted in other
        bioinformatics fields like automated deployment systems, workflow orchestration,
        or the use of software containers. We present here a comprehensive exercise
        to bring biomolecular simulations to the “bioinformatics way of working”.
        The exercise has led to the development of the BioExcel Building Blocks (BioBB)
        library. BioBB’s are built as Python wrappers to provide an interoperable
        architecture. BioBB’s have been integrated in a chain of usual software management
        tools to generate data ontologies, documentation, installation packages, software
        containers and ways of integration with workflow managers, that make them
        usable in most computational environments.
      authors:
      - name: Andrio P.
      - name: Hospital A.
      - name: Conejero J.
      - name: Jorda L.
      - name: Del Pino M.
      - name: Codo L.
      - name: Soiland-Reyes S.
      - name: Goble C.
      - name: Lezzi D.
      - name: Badia R.M.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 39
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Data
      title: BioExcel Building Blocks, a software library for interoperable biomolecular
        simulation workflows
    note: BioExcel Building Blocks (BioBB)
    pmcid: PMC6736963
    pmid: '31506435'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: biobb
    type: uses
  - biotoolsID: nglview
    type: uses
  - biotoolsID: classical_molecular_interaction_potentials_cmip
    type: uses
  toolType:
  - Workflow
  topic:
  - term: Biomolecular simulation
    uri: http://edamontology.org/topic_3892
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-08-31T07:04:02.274853Z'
  biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_protein_conformational_transitions
  biotoolsID: bioexcel_building_blocks_tutorials_protein_conformational_transitions
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital Gasch
    note: null
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: https://orcid.org/0000-0003-0513-0288
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.irbbarcelona.org/es/research/genis-bayarri
  - email: null
    fundrefid: null
    gridid: null
    name: BioExcel CoE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://bioexcel.eu/
  description: This tutorial aims to illustrate the process of computing a conformational
    transition between two known structural conformations of a protein, step by step,
    using the BioExcel Building Blocks (biobb).
  documentation:
  - note: Documentation in Read the Docs
    type:
    - Other
    url: https://biobb-wf-godmd.readthedocs.io/en/latest/index.html
  download:
  - note: Source Code in GitHub
    type: Source code
    url: https://github.com/bioexcel/biobb_wf_godmd
    version: '1.0'
  - note: BioExcel Binder
    type: VM image
    url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_godmd/main?filepath=biobb_wf_godmd%2Fnotebooks%2Fbiobb_wf_godmd.ipynb
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Spain
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Structure analysis
      uri: http://edamontology.org/operation_2480
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Trajectory visualization
      uri: http://edamontology.org/operation_3890
    output:
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: mdcrd
        uri: http://edamontology.org/format_3878
      - term: PCAzip
        uri: http://edamontology.org/format_3874
  homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:42:14.496379Z'
  license: Apache-2.0
  link:
  - note: Tutorial in HTML
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd
  - note: Tutorial in Read the Docs
    type:
    - Other
    url: https://biobb-wf-godmd.readthedocs.io/en/latest/index.html
  - note: Source Code in GitHub
    type:
    - Repository
    url: https://github.com/bioexcel/biobb_wf_godmd
  maturity: Emerging
  name: 'BioExcel Building Blocks tutorials: Protein Conformational Transitions'
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication:
  - doi: 10.1038/s41597-019-0177-4
    metadata:
      abstract: In the recent years, the improvement of software and hardware performance
        has made biomolecular simulations a mature tool for the study of biological
        processes. Simulation length and the size and complexity of the analyzed systems
        make simulations both complementary and compatible with other bioinformatics
        disciplines. However, the characteristics of the software packages used for
        simulation have prevented the adoption of the technologies accepted in other
        bioinformatics fields like automated deployment systems, workflow orchestration,
        or the use of software containers. We present here a comprehensive exercise
        to bring biomolecular simulations to the “bioinformatics way of working”.
        The exercise has led to the development of the BioExcel Building Blocks (BioBB)
        library. BioBB’s are built as Python wrappers to provide an interoperable
        architecture. BioBB’s have been integrated in a chain of usual software management
        tools to generate data ontologies, documentation, installation packages, software
        containers and ways of integration with workflow managers, that make them
        usable in most computational environments.
      authors:
      - name: Andrio P.
      - name: Hospital A.
      - name: Conejero J.
      - name: Jorda L.
      - name: Del Pino M.
      - name: Codo L.
      - name: Soiland-Reyes S.
      - name: Goble C.
      - name: Lezzi D.
      - name: Badia R.M.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 39
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Data
      title: BioExcel Building Blocks, a software library for interoperable biomolecular
        simulation workflows
    note: BioExcel Building Blocks (BioBB)
    pmcid: PMC6736963
    pmid: '31506435'
    type:
    - Other
    version: null
  - doi: 10.1093/bioinformatics/btt324
    metadata:
      abstract: 'Motivation: A new algorithm to trace conformational transitions in
        proteins is presented. The method uses discrete molecular dynamics as engine
        to sample protein conformational space. A multiple minima Go-like potential
        energy function is used in combination with several enhancing sampling strategies,
        such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics.
        The method, which shows an unprecedented computational efficiency, is able
        to trace a wide range of known experimental transitions. Contrary to simpler
        methods our strategy does not introduce distortions in the chemical structure
        of the protein and is able to reproduce well complex non-linear conformational
        transitions. The method, called GOdMD, can easily introduce additional restraints
        to the transition (presence of ligand, known intermediate, known maintained
        contacts, ...) and is freely distributed to the community through the Spanish
        National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD).Availability:
        Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.Contact:
        or modesto@mmb.pcb.ub.esSupplementary information: Supplementary data are
        available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford
        University Press.'
      authors:
      - name: Sfriso P.
      - name: Hospital A.
      - name: Emperador A.
      - name: Orozco M.
      citationCount: 28
      date: '2013-08-15T00:00:00Z'
      journal: Bioinformatics
      title: Exploration of conformational transition pathways from coarse-grained
        simulations
    note: GOdMD method
    pmcid: null
    pmid: '23740746'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: biobb
    type: uses
  - biotoolsID: godmd
    type: uses
  - biotoolsID: water
    type: uses
  toolType:
  - Workflow
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Biomolecular simulation
    uri: http://edamontology.org/topic_3892
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2021-11-30T11:10:36.326367Z'
  biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_protein-ligand_docking
  biotoolsID: bioexcel_building_blocks_tutorials_protein-ligand_docking
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BioExcel Center of Excellence for Computational Biomolecular Research
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://www.bioexcel.eu
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: https://orcid.org/0000-0003-0513-0288
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/genis-bayarri
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: null
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  description: This tutorial aims to illustrate the process of protein-ligand docking,
    step by step, using the BioExcel Building Blocks library (biobb).
  documentation:
  - note: Read the Docs Workflow Documentation (PDB Cluster90 Binding Site Version)
    type:
    - Other
    url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/cluster_bs_tutorial.html
  - note: Read the Docs Workflow Documentation (PDBe REST-API Binding Site Version)
    type:
    - Other
    url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.html
  - note: Read the Docs Workflow Documentation (Fpocket Binding Site Version)
    type:
    - Other
    url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/fpocket_tutorial.html
  download:
  - note: null
    type: Source code
    url: https://github.com/bioexcel/biobb_wf_virtual-screening
    version: '1.0'
  editPermission:
    authors:
    - gelpi@ub.edu
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  - UK
  elixirPlatform:
  - Interoperability
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: SDF
        uri: http://edamontology.org/format_3814
    note: null
    operation:
    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    output:
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
  homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bs
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:42:12.777446Z'
  license: Apache-2.0
  link:
  - note: Tutorial in HTML (PDB Cluster90 Binding Site Version)
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bs
  - note: Tutorial in Read The Docs (PDB Cluster90 Binding Site Version)
    type:
    - Other
    url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/cluster_bs_tutorial.html
  - note: Source Code in GitHub
    type:
    - Repository
    url: https://github.com/bioexcel/biobb_wf_virtual-screening
  - note: Tutorial in HTML (PDBe REST-API Binding Site Version)
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_ebi
  - note: Tutorial in Read the Docs (PDBe REST-API Binding Site Version)
    type:
    - Other
    url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.html
  - note: Tutorial in HTML (Fpocket Binding Site Version)
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_fpocket
  - note: Tutorial in Read the Docs (Fpocket Binding Site Version)
    type:
    - Other
    url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/fpocket_tutorial.html
  maturity: Emerging
  name: 'BioExcel Building Blocks tutorials: Protein-ligand Docking'
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication:
  - doi: 10.1038/s41597-019-0177-4
    metadata:
      abstract: In the recent years, the improvement of software and hardware performance
        has made biomolecular simulations a mature tool for the study of biological
        processes. Simulation length and the size and complexity of the analyzed systems
        make simulations both complementary and compatible with other bioinformatics
        disciplines. However, the characteristics of the software packages used for
        simulation have prevented the adoption of the technologies accepted in other
        bioinformatics fields like automated deployment systems, workflow orchestration,
        or the use of software containers. We present here a comprehensive exercise
        to bring biomolecular simulations to the “bioinformatics way of working”.
        The exercise has led to the development of the BioExcel Building Blocks (BioBB)
        library. BioBB’s are built as Python wrappers to provide an interoperable
        architecture. BioBB’s have been integrated in a chain of usual software management
        tools to generate data ontologies, documentation, installation packages, software
        containers and ways of integration with workflow managers, that make them
        usable in most computational environments.
      authors:
      - name: Andrio P.
      - name: Hospital A.
      - name: Conejero J.
      - name: Jorda L.
      - name: Del Pino M.
      - name: Codo L.
      - name: Soiland-Reyes S.
      - name: Goble C.
      - name: Lezzi D.
      - name: Badia R.M.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 39
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Data
      title: BioExcel Building Blocks, a software library for interoperable biomolecular
        simulation workflows
    note: null
    pmcid: PMC6736963
    pmid: '31506435'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: biobb
    type: uses
  - biotoolsID: autodock_vina
    type: uses
  - biotoolsID: fpocket
    type: uses
  - biotoolsID: pdbe
    type: uses
  toolType:
  - Workflow
  topic:
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-09-26T23:26:58.411470Z'
  biotoolsCURIE: biotools:planet_microbe
  biotoolsID: planet_microbe
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: bhurwitz@arizona.edu
    fundrefid: null
    gridid: null
    name: Bonnie Hurwitz
    note: Professor at the University of Arizona known for her work in cyberinfrastructure
      development.
    orcidid: https://orcid.org/0000-0001-8699-957X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.hurwitzlab.org/
  - email: aponsero@arizona.edu
    fundrefid: null
    gridid: null
    name: Alise Ponsero
    note: null
    orcidid: https://orcid.org/0000-0002-4125-7561
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: kblumberg@arizona.edu
    fundrefid: null
    gridid: null
    name: Kai Blumberg
    note: null
    orcidid: https://orcid.org/0000-0002-3410-4655
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: mattmiller899@arizona.edu
    fundrefid: null
    gridid: null
    name: Matthew Miller
    note: null
    orcidid: https://orcid.org/0000-0002-3491-8763
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: mbomhoff@arizona.edu
    fundrefid: null
    gridid: null
    name: Matthew Bomhoff
    note: null
    orcidid: https://orcid.org/0000-0002-8014-9184
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: kyclark@arizona.edu
    fundrefid: null
    gridid: null
    name: Ken Youens-Clark
    note: null
    orcidid: https://orcid.org/0000-0001-9961-144X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: Enabling the discovery and integration of oceanographic ‘omics, environmental
    and physiochemical data layers.
  documentation: []
  download:
  - note: Source code for the website
    type: Source code
    url: https://github.com/hurwitzlab/planet-microbe-app
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    output: []
  homepage: https://www.planetmicrobe.org/
  homepage_status: 0
  language:
  - Elm
  lastUpdate: '2024-11-24T14:39:10.273022Z'
  license: MIT
  link:
  - note: Planet Microbe Application
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-app
  - note: Planet Microbe frictionless data packages
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-datapackages
  - note: Planet Microbe ontology
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-ontology
  - note: Functional Annotation Pipeline
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-functional-annotation
  - note: Semantic web analysis
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-semantic-web-analysis
  maturity: Mature
  name: Planet Microbe
  operatingSystem:
  - Linux
  otherID: []
  owner: bhurwitz
  publication:
  - doi: 10.1093/nar/gkaa637
    metadata:
      abstract: In recent years, large-scale oceanic sequencing efforts have provided
        a deeper understanding of marine microbial communities and their dynamics.
        These research endeavors require the acquisition of complex and varied datasets
        through large, interdisciplinary and collaborative efforts. However, no unifying
        framework currently exists for the marine science community to integrate sequencing
        data with physical, geological, and geochemical datasets. Planet Microbe is
        a web-based platform that enables data discovery from curated historical and
        ongoing oceanographic sequencing efforts. In Planet Microbe, each 'omics sample
        is linked with other biological and physiochemical measurements collected
        for the same water samples or during the same sample collection event, to
        provide a broader environmental context. This work highlights the need for
        curated aggregation efforts that can enable new insights into high-quality
        metagenomic datasets. Planet Microbe is freely accessible from https://www.planetmicrobe.org/.
      authors:
      - name: Ponsero A.J.
      - name: Bomhoff M.
      - name: Blumberg K.
      - name: Youens-Clark K.
      - name: Herz N.M.
      - name: Wood-Charlson E.M.
      - name: Delong E.F.
      - name: Hurwitz B.L.
      citationCount: 13
      date: '2021-01-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Planet Microbe: A platform for marine microbiology to discover and analyze
        interconnected ''omics and environmental data'''
    note: In recent years, large-scale oceanic sequencing efforts have provided a
      deeper understanding of marine microbial communities and their dynamics. These
      research endeavors require the acquisition of complex and varied datasets through
      large, interdisciplinary and collaborative efforts. However, no unifying framework
      currently exists for the marine science community to integrate sequencing data
      with physical, geological, and geochemical datasets. Planet Microbe is a web-based
      platform that enables data discovery from curated historical and on-going oceanographic
      sequencing efforts. In Planet Microbe, each 'omics sample is linked with other
      biological and physiochemical measurements collected for the same water samples
      or during the same sample collection event, to provide a broader environmental
      context. This work highlights the need for curated aggregation efforts that
      can enable new insights into high-quality metagenomic datasets.
    pmcid: PMC7778950
    pmid: '32735679'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Bioinformatics portal
  topic:
  - term: Marine biology
    uri: http://edamontology.org/topic_3387
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-09-26T23:32:38.521840Z'
  biotoolsCURIE: biotools:planetmicrobe
  biotoolsID: planetmicrobe
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: bhurwitz@arizona.edu
    fundrefid: null
    gridid: null
    name: Bonnie Hurwitz
    note: Professor at the University of Arizona known for her work in cyberinfrastructure
      development.
    orcidid: https://orcid.org/0000-0001-8699-957X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.hurwitzlab.org/
  - email: aponsero@arizona.edu
    fundrefid: null
    gridid: null
    name: Alise Ponsero
    note: null
    orcidid: https://orcid.org/0000-0002-4125-7561
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: kblumberg@arizona.edu
    fundrefid: null
    gridid: null
    name: Kai Blumberg
    note: null
    orcidid: https://orcid.org/0000-0002-3410-4655
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: mattmiller899@arizona.edu
    fundrefid: null
    gridid: null
    name: Matthew Miller
    note: null
    orcidid: https://orcid.org/0000-0002-3491-8763
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: mbomhoff@arizona.edu
    fundrefid: null
    gridid: null
    name: Matthew Bomhoff
    note: null
    orcidid: https://orcid.org/0000-0002-8014-9184
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: kyclark@arizona.edu
    fundrefid: null
    gridid: null
    name: Ken Youens-Clark
    note: null
    orcidid: https://orcid.org/0000-0001-9961-144X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: Enabling the discovery and integration of oceanographic ‘omics, environmental
    and physiochemical data layers.
  documentation:
  - note: Documentation on how to use the website
    type:
    - General
    url: https://hurwitzlab.gitbook.io/planet-microbe-documentation/
  download:
  - note: Source code for the website
    type: Source code
    url: https://github.com/hurwitzlab/planet-microbe-app
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    output: []
  homepage: https://www.planetmicrobe.org/
  homepage_status: 0
  language:
  - Elm
  lastUpdate: '2024-11-24T14:39:08.746037Z'
  license: MIT
  link:
  - note: Planet Microbe Application
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-app
  - note: Planet Microbe frictionless data packages
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-datapackages
  - note: Planet Microbe ontology
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-ontology
  - note: Functional Annotation Pipeline
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-functional-annotation
  - note: Semantic web analysis
    type:
    - Repository
    url: https://github.com/hurwitzlab/planet-microbe-semantic-web-analysis
  maturity: Mature
  name: Planet Microbe
  operatingSystem:
  - Linux
  otherID: []
  owner: bhurwitz
  publication:
  - doi: 10.1093/nar/gkaa637
    metadata:
      abstract: In recent years, large-scale oceanic sequencing efforts have provided
        a deeper understanding of marine microbial communities and their dynamics.
        These research endeavors require the acquisition of complex and varied datasets
        through large, interdisciplinary and collaborative efforts. However, no unifying
        framework currently exists for the marine science community to integrate sequencing
        data with physical, geological, and geochemical datasets. Planet Microbe is
        a web-based platform that enables data discovery from curated historical and
        ongoing oceanographic sequencing efforts. In Planet Microbe, each 'omics sample
        is linked with other biological and physiochemical measurements collected
        for the same water samples or during the same sample collection event, to
        provide a broader environmental context. This work highlights the need for
        curated aggregation efforts that can enable new insights into high-quality
        metagenomic datasets. Planet Microbe is freely accessible from https://www.planetmicrobe.org/.
      authors:
      - name: Ponsero A.J.
      - name: Bomhoff M.
      - name: Blumberg K.
      - name: Youens-Clark K.
      - name: Herz N.M.
      - name: Wood-Charlson E.M.
      - name: Delong E.F.
      - name: Hurwitz B.L.
      citationCount: 13
      date: '2021-01-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Planet Microbe: A platform for marine microbiology to discover and analyze
        interconnected ''omics and environmental data'''
    note: In recent years, large-scale oceanic sequencing efforts have provided a
      deeper understanding of marine microbial communities and their dynamics. These
      research endeavors require the acquisition of complex and varied datasets through
      large, interdisciplinary and collaborative efforts. However, no unifying framework
      currently exists for the marine science community to integrate sequencing data
      with physical, geological, and geochemical datasets. Planet Microbe is a web-based
      platform that enables data discovery from curated historical and on-going oceanographic
      sequencing efforts. In Planet Microbe, each 'omics sample is linked with other
      biological and physiochemical measurements collected for the same water samples
      or during the same sample collection event, to provide a broader environmental
      context. This work highlights the need for curated aggregation efforts that
      can enable new insights into high-quality metagenomic datasets.
    pmcid: PMC7778950
    pmid: '32735679'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Bioinformatics portal
  topic:
  - term: Marine biology
    uri: http://edamontology.org/topic_3387
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2024-01-28T18:03:20.705547Z'
  biotoolsCURIE: biotools:coconat
  biotoolsID: coconat
  collectionID:
  - Bologna Biocomputing Group
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-BOLOGNA
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: castrense.savojardo2@unibo.it
    fundrefid: null
    gridid: null
    name: Castrense Savojardo
    note: null
    orcidid: https://orcid.org/0000-0002-7359-0633
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: pierluigi.martelli@unibo.it
    fundrefid: null
    gridid: null
    name: Pier Luigi Martelli
    note: null
    orcidid: https://orcid.org/0000-0002-0274-5669
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: CoCoNat is a novel deep-learning based method for predicting coiled-coil
    regions, register annotation and oligomenrization state. CoCoNat adopts a sequence
    encoding based on two state-of-the-art protein language models and a deep-learning
    architetcure to perform prediction.
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://github.com/BolognaBiocomp/coconat
  - note: null
    type:
    - User manual
    url: https://coconat.biocomp.unibo.it/help/
  download:
  - note: null
    type: Source code
    url: https://github.com/BolognaBiocomp/coconat
    version: '1.0'
  editPermission:
    authors:
    - ELIXIR-ITA-BOLOGNA
    - savo
    type: group
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Protein super-secondary structure prediction
      uri: http://edamontology.org/operation_0268
    output:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://coconat.biocomp.unibo.it
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:10:14.901849Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: CoCoNat
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ELIXIR-ITA-BOLOGNA
  publication:
  - doi: 10.1093/bioinformatics/btad495
    metadata:
      abstract: 'Motivation: Coiled-coil domains (CCD) are widespread in all organisms
        and perform several crucial functions. Given their relevance, the computational
        detection of CCD is very important for protein functional annotation. State-of-the-art
        prediction methods include the precise identification of CCD boundaries, the
        annotation of the typical heptad repeat pattern along the coiled-coil helices
        as well as the prediction of the oligomerization state. Results: In this article,
        we describe CoCoNat, a novel method for predicting coiled-coil helix boundaries,
        residue-level register annotation, and oligomerization state. Our method encodes
        sequences with the combination of two state-of-the-art protein language models
        and implements a three-step deep learning procedure concatenated with a Grammatical-Restrained
        Hidden Conditional Random Field for CCD identification and refinement. A final
        neural network predicts the oligomerization state. When tested on a blind
        test set routinely adopted, CoCoNat obtains a performance superior to the
        current state-of-the-art both for residue-level and segment-level CCD. CoCoNat
        significantly outperforms the most recent state-of-the-art methods on register
        annotation and prediction of oligomerization states.'
      authors:
      - name: Madeo G.
      - name: Savojardo C.
      - name: Manfredi M.
      - name: Martelli P.L.
      - name: Casadio R.
      citationCount: 5
      date: '2023-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'CoCoNat: a novel method based on deep learning for coiled-coil prediction'
    note: null
    pmcid: PMC10425188
    pmid: '37540220'
    type:
    - Primary
    version: null
  - doi: 10.21769/BioProtoc.4935
    metadata:
      abstract: 'Coiled-coil domains (CCDs) are structural motifs observed in proteins
        in all organisms that perform several crucial functions. The computational
        identification of CCD segments over a protein sequence is of great importance
        for its functional characterization. This task can essentially be divided
        into three separate steps: the detection of segment boundaries, the annotation
        of the heptad repeat pattern along the segment, and the classification of
        its oligomerization state. Several methods have been proposed over the years
        addressing one or more of these predictive steps. In this protocol, we illustrate
        how to make use of CoCoNat, a novel approach based on protein language models,
        to characterize CCDs. CoCoNat is, at its release (August 2023), the state
        of the art for CCD detection. The web server allows users to submit input
        protein sequences and visualize the predicted domains after a few minutes.
        Optionally, precomputed segments can be provided to the model, which will
        predict the oligomerization state for each of them. CoCoNat can be easily
        integrated into biological pipelines by downloading the standalone version,
        which provides a single executable script to produce the output.'
      authors:
      - name: Manfredi M.
      - name: Savojardo C.
      - name: Martelli P.L.
      - name: Casadio R.
      citationCount: 0
      date: '2024-02-20T00:00:00Z'
      journal: Bio-protocol
      title: 'CoCoNat: A Deep Learning–Based Tool for the Prediction of Coiled-coil
        Domains in Protein Sequences'
    note: null
    pmcid: PMC10883893
    pmid: '38405078'
    type:
    - Usage
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2024-10-24T04:20:54.023066Z'
  biotoolsCURIE: biotools:plasgo
  biotoolsID: plasgo
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'PlasGO: a Python library (Linux or Ubuntu only) for predicting cluster-level
    Gene Ontology (GO) terms of plasmid-encoded proteins.'
  documentation: []
  download:
  - note: null
    type: Software package
    url: https://github.com/Orin-beep/PlasGO
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Orin-beep/PlasGO
  homepage_status: 0
  language: []
  lastUpdate: '2024-10-24T04:20:54.026192Z'
  license: null
  link: []
  maturity: null
  name: PlasGO
  operatingSystem: []
  otherID: []
  owner: yongxinji2
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2024-10-19T08:26:31.153400Z'
  biotoolsCURIE: biotools:get_mnv
  biotoolsID: get_mnv
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs)
    within the same codon in genomic sequences. MNVs occur when multiple Single Nucleotide
    Variants (SNVs) are present within the same codon, leading to the translation
    of a different amino acid. This tool addresses limitations in current annotation
    programs like ANNOVAR or SnpEff, which are primarily designed to work with individual
    SNVs and might overlook the actual amino acid changes resulting from MNVs.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/PathoGenOmics-Lab/get_MNV/wiki
  download:
  - note: null
    type: Binaries
    url: https://github.com/PathoGenOmics-Lab/get_MNV/releases/download/1.0.0/get_mnv
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: get_mnv [OPTIONS] --vcf <VCF_FILE> --fasta <FASTA_FILE> --genes <GENES_FILE>
    input:
    - data:
        term: Sequence map
        uri: http://edamontology.org/data_1279
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: SNP annotation
      uri: http://edamontology.org/operation_3661
    output:
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/PathoGenOmics-Lab/get_mnv
  homepage_status: 0
  language:
  - Other
  lastUpdate: '2024-10-19T08:26:31.156201Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/PathoGenOmics-Lab/get_mnv
  maturity: Emerging
  name: get_MNV
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: paururo
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2024-05-20T10:12:42.015384Z'
  biotoolsCURIE: biotools:deepdefense
  biotoolsID: deepdefense
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: software tool for the annotation and discovery of novel immune systems
    in prokaryotes
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/SvenHauns/Deepdefense
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output: []
  homepage: https://github.com/SvenHauns/Deepdefense
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-05-20T10:12:42.017753Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/SvenHauns/Deepdefense
  maturity: null
  name: Deepdefense
  operatingSystem: []
  otherID: []
  owner: haunssv
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Biology
    uri: http://edamontology.org/topic_3070
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-11-17T03:14:31.662275Z'
  biotoolsCURIE: biotools:Scan
  biotoolsID: Scan
  collectionID:
  - Cancer
  confidence_flag: null
  cost: null
  credit:
  - email: zhangjunpeng411@gmail.com
    fundrefid: null
    gridid: null
    name: Junpeng Zhang
    note: null
    orcidid: https://orcid.org/0000-0001-6127-9701
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Scanning sample-specific miRNA regulation from bulk and single-cell
    RNA-sequencing data
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/zhangjunpeng411/Scan
  download:
  - note: null
    type: Source code
    url: https://github.com/zhangjunpeng411/Scan
    version: '1.0'
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: null
    operation:
    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    - term: miRNA expression analysis
      uri: http://edamontology.org/operation_3792
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format: []
  homepage: https://github.com/zhangjunpeng411/Scan
  homepage_status: 0
  language:
  - R
  - MATLAB
  lastUpdate: '2023-11-17T07:03:20.353905Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/zhangjunpeng411/Scan
  maturity: null
  name: Scan
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: zhangjunpeng
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-08-01T00:26:20.371769Z'
  biotoolsCURIE: biotools:GERONIMO
  biotoolsID: GERONIMO
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: agata.kilar@gmail.com
    fundrefid: null
    gridid: null
    name: Agata Kilar
    note: null
    orcidid: https://orcid.org/0000-0003-3876-6581
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: GERONIMO is a bioinformatics pipeline designed to conduct high-throughput
    homology searches of structural genes using covariance models. These models are
    based on the alignment of sequences and the consensus of secondary structures.
    The pipeline is built using Snakemake, a workflow management tool that allows
    for the reproducible execution of analyses on various computational platforms.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/amkilar/GERONIMO.git
  download:
  - note: null
    type: Source code
    url: https://github.com/amkilar/GERONIMO.git
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/amkilar/GERONIMO.git
  homepage_status: 0
  language:
  - Python
  - R
  - Bash
  lastUpdate: '2023-08-01T00:36:04.641143Z'
  license: MIT
  link: []
  maturity: Mature
  name: GERONIMO
  operatingSystem:
  - Windows
  - Linux
  otherID: []
  owner: amkilar
  publication: []
  relation:
  - biotoolsID: infernal
    type: uses
  toolType:
  - Workflow
  - Command-line tool
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2021-09-20T06:49:28.552326Z'
  biotoolsCURIE: biotools:mirkit
  biotoolsID: mirkit
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: fpsom@certh.gr
    fundrefid: null
    gridid: null
    name: Fotis Psomopoulos
    note: null
    orcidid: https://orcid.org/0000-0002-0222-4273
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: miRkit is an open source framework written in R, that allows for the
    comprehensive analysis of RT-PCR data, from the processing of raw data to a functional
    analysis of the produced results. The main goal of the tool is to provide an assessment
    of the samples’ quality, perform data normalization by endogenous and exogenous
    miRNAs, and facilitate differential and functional enrichment analysis. The tool
    offers fast execution times with low memory usage, can perform the full analysis
    from the raw RT-PCR data to functional analysis of targeted genes, and is specifically
    designed to support the popular miScript miRNA PCR Array (Qiagen) technology.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/BiodataAnalysisGroup/miRkit/blob/main/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/BiodataAnalysisGroup/miRkit
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: raw
        uri: http://edamontology.org/format_1957
      - term: R script
        uri: http://edamontology.org/format_3999
    note: null
    operation:
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: miRNA expression analysis
      uri: http://edamontology.org/operation_3792
    output: []
  homepage: https://github.com/BiodataAnalysisGroup/miRkit
  homepage_status: 0
  language: []
  lastUpdate: '2022-12-01T22:34:37.796805Z'
  license: MIT
  link: []
  maturity: Mature
  name: mirKit
  operatingSystem: []
  otherID: []
  owner: fpsom
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2019-10-16T13:13:42Z'
  biotoolsCURIE: biotools:CWL_VM_environment
  biotoolsID: CWL_VM_environment
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: famaladoss@ebi.ac.uk
    fundrefid: null
    gridid: null
    name: Felix Xavier Amaladoss
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: CWL VM environment is a repository which can be deployed on cloud to
    execute Biobb Mutations Workflow.
  documentation: []
  download:
  - note: BioExcel_ECP_Application;name:CWL VM environment;teamName:BioExcel Embassy;config:CWL
      biobb_wf_mutations
    type: VM image
    url: https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwl
    version: '1.0'
  editPermission:
    authors:
    - adam.hospital@irbbarcelona.org
    - felixamaladoss
    - johnnyfelix
    - felixebi
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwl
  homepage_status: 0
  language: []
  lastUpdate: '2022-11-29T23:23:26.018525Z'
  license: null
  link: []
  maturity: null
  name: Biobb Mutations Workflow
  operatingSystem:
  - Linux
  otherID: []
  owner: felixamaladoss
  publication: []
  relation: []
  toolType:
  - Workbench
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  validated: 0
  version:
  - '1.0'
- accessibility: Open access (with restrictions)
  additionDate: '2015-10-29T14:34:58Z'
  biotoolsCURIE: biotools:xeml-lab
  biotoolsID: xeml-lab
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Benjamin Dartigues
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Yves Gibon
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Cecile Cabasson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: UMR 1332 - Biologie du Fruit et Pathologie
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Centre de Bioinformatique de Bordeaux (CBiB)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Macha Nikolski
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Alexis Groppi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: The web application Linda offers a complete tool for entering and managing
    metadata associated with a phenotyping experiment on plants. It thus makes it
    possible to intuitively describe experimental related information such as, for
    example, the experimental design, the growth protocols, the environmental variable
    measurements, etc. Linda is coupled with a database that stores this information
    in a structured manneer using oriented graphs. This database uses reference ontologies
    (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated to this type
    of experiment such as the Minimal Information About Plant Phenotyping Experiment
    (MIAPPE) standard. Data sharing is facilitated on the one hand by respecting the
    FAIR principles (Findable Accessible Interoperable Reusable) and oon the other
    hand, by exporting this metadata relating to the experiment in tabulated formats
    or formatted for submission in the international databases (ISA-tab).
  documentation:
  - note: null
    type:
    - General
    - Citation instructions
    - General
    url: https://services.cbib.u-bordeaux.fr/linda
  download:
  - note: null
    type: Tool wrapper (Other)
    url: https://services.cbib.u-bordeaux.fr/linda
    version: '1.0'
  editPermission:
    authors:
    - bdartigues
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: The web application Linda offers a complete tool for entering and managing
      metadata associated with a phenotyping experiment on plants. It thus makes it
      possible to intuitively describe experimental related information such as, for
      example, the experimental design, the growth protocols, the environmental variable
      measurements, etc. Linda is coupled with a database that stores this information
      in a structured manneer using oriented graphs. This database uses reference
      ontologies (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated
      to this type of experiment such as the Minimal Information About Plant Phenotyping
      Experiment (MIAPPE) standard. Data sharing is facilitated on the one hand by
      respecting the FAIR principles (Findable Accessible Interoperable Reusable)
      and oon the other hand, by exporting this metadata relating to the experiment
      in tabulated formats or formatted for submission in the international databases
      (ISA-tab).
    operation:
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    output: []
  homepage: https://services.cbib.u-bordeaux.fr/linda/
  homepage_status: 0
  language:
  - JavaScript
  - Bash
  - Python
  - Other
  lastUpdate: '2022-09-27T14:48:43.394660Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://services.cbib.u-bordeaux.fr/linda/
  maturity: Emerging
  name: Linda
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: bdartigues
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2022-03-24T09:57:50.414985Z'
  biotoolsCURIE: biotools:mistic_predictor
  biotoolsID: mistic_predictor
  collectionID:
  - Rare Disease
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: kchennen@unistra.fr
    fundrefid: null
    gridid: null
    name: Kirsley Chennen
    note: null
    orcidid: https://orcid.org/0000-0001-9268-6748
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Thomas Weber
    note: null
    orcidid: https://orcid.org/0000-0002-0807-6363
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: olivier.poch@unistra.fr
    fundrefid: null
    gridid: null
    name: Olivier Poch
    note: null
    orcidid: https://orcid.org/0000-0002-7134-3217
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: MISTIC (MISsense deleTeriousness predICtor), a prediction tool to reveal
    disease-relevant deleterious missense variants based on an original combination
    of two complementary machine learning algorithms using a soft voting system that
    integrates 113 missense features, ranging from multi-ethnic minor allele frequencies
    and evolutionary conservation, to physiochemical and biochemical properties of
    amino acids.
  documentation: []
  download:
  - note: null
    type: Downloads page
    url: http://lbgi.fr/mistic/download
    version: '1.0'
  - note: null
    type: API specification
    url: https://lbgi.fr/api/index.rvt?api=mistic
    version: '1.0'
  editPermission:
    authors:
    - kchennen
    type: private
  elixirCommunity:
  - Rare Diseases
  elixirNode:
  - France
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    - term: Variant prioritisation
      uri: http://edamontology.org/operation_3226
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    output: []
  homepage: http://lbgi.fr/mistic
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2022-03-24T13:12:19.605062Z'
  license: MIT
  link: []
  maturity: Mature
  name: MISTIC
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: kchennen
  publication:
  - doi: 10.1371/journal.pone.0236962
    metadata:
      abstract: 'Copyright: © 2020 Chennen et al. This is an open access article distributed
        under the terms of the Creative Commons Attribution License, which permits
        unrestricted use, distribution, and reproduction in any medium, provided the
        original author and source are credited.The diffusion of next-generation sequencing
        technologies has revolutionized research and diagnosis in the field of rare
        Mendelian disorders, notably via whole-exome sequencing (WES). However, one
        of the main issues hampering achievement of a diagnosis via WES analyses is
        the extended list of variants of unknown significance (VUS), mostly composed
        of missense variants. Hence, improved solutions are needed to address the
        challenges of identifying potentially deleterious variants and ranking them
        in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor),
        a new prediction tool based on an original combination of two complementary
        machine learning algorithms using a soft voting system that integrates 113
        missense features, ranging from multi-ethnic minor allele frequencies and
        evolutionary conservation, to physiochemical and biochemical properties of
        amino acids. Our approach also uses training sets with a wide spectrum of
        variant profiles, including both high-confidence positive (deleterious) and
        negative (benign) variants. Compared to recent state-of-the-art prediction
        tools in various benchmark tests and independent evaluation scenarios, MISTIC
        exhibits the best and most consistent performance, notably with the highest
        AUC value (> 0.95). Importantly, MISTIC maintains its high performance in
        the specific case of discriminating deleterious variants from benign variants
        that are rare or population-specific. In a clinical context, MISTIC drastically
        reduces the list of VUS (<30%) and significantly improves the ranking of “causative”
        deleterious variants. Pre-computed MISTIC scores for all possible human missense
        variants are available at http://lbgi.fr/mistic.'
      authors:
      - name: Chennen K.
      - name: Weber T.
      - name: Lornage X.
      - name: Kress A.
      - name: Bohm J.
      - name: Thompson J.
      - name: Laporte J.
      - name: Poch O.
      citationCount: 6
      date: '2020-07-01T00:00:00Z'
      journal: PLoS ONE
      title: 'MISTIC: A prediction tool to reveal disease-relevant deleterious missense
        variants'
    note: null
    pmcid: PMC7394404
    pmid: '32735577'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Web application
  - Web API
  - Script
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Exome sequencing
    uri: http://edamontology.org/topic_3676
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2021-09-06T16:10:55Z'
  biotoolsCURIE: biotools:viqor
  biotoolsID: viqor
  collectionID:
  - Proteomics
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: vasileios@bmb.sdu.dk
    fundrefid: null
    gridid: null
    name: Vasileios Tsiamis
    note: null
    orcidid: https://orcid.org/0000-0003-1359-5253
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Documentor
    - Maintainer
    - Primary contact
    - Support
    url: null
  - email: veits@bmb.sdu.dk
    fundrefid: null
    gridid: null
    name: Veit Schwämmle
    note: null
    orcidid: https://orcid.org/0000-0002-9708-6722
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    - Provider
    url: null
  description: VIQoR, is a user-friendly web service for Visually supervised protein
    Inference and protein Quantification implemented in R. The Shiny web interface
    integrates the post-identification processes involved in protein inference and
    relative protein abundance summarization, along with smart and novel interactive
    visualization modules to support the common researchers with a straight-forward
    tool for protein quantification, data browsing and data inspection.
  documentation:
  - note: null
    type:
    - User manual
    url: https://bitbucket.org/vtsiamis/viqor/src/master/Manual.pdf
  download:
  - note: null
    type: Source code
    url: https://bitbucket.org/vtsiamis/viqor/downloads/
    version: '1.0'
  editPermission:
    authors: []
    type: public
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Denmark
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence set (protein)
        uri: http://edamontology.org/data_1233
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: null
    operation:
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    - term: Filtering
      uri: http://edamontology.org/operation_3695
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Mapping
      uri: http://edamontology.org/operation_2429
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Protein quantification
      uri: http://edamontology.org/operation_3630
    - term: Expression correlation analysis
      uri: http://edamontology.org/operation_3463
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: Dendrogram visualisation
      uri: http://edamontology.org/operation_2938
    - term: Sequence assembly visualisation
      uri: http://edamontology.org/operation_3184
    output:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: http://computproteomics.bmb.sdu.dk:443/app_direct/VIQoR/
  homepage_status: 0
  language:
  - R
  - JavaScript
  lastUpdate: '2022-03-20T07:04:44.038383Z'
  license: Apache-2.0
  link:
  - note: Repository of source code and docker file.
    type:
    - Repository
    url: https://bitbucket.org/vtsiamis/viqor/
  - note: null
    type:
    - Service
    url: http://computproteomics.bmb.sdu.dk:8192/app_direct/VIQoR/
  maturity: Mature
  name: VIQoR
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: vtsiamis
  publication:
  - doi: 10.1101/2021.06.01.446512
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  - Script
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  - term: Protein modifications
    uri: http://edamontology.org/topic_0601
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2022-03-11T12:50:46.723332Z'
  biotoolsCURIE: biotools:spacnacs
  biotoolsID: spacnacs
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: joaquin.dopazo@juntadeandalucia.es
    fundrefid: null
    gridid: null
    name: Joaquín Dopazo
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: SPACNACS is a crowdsourcing initiative to provide information about
    Copy Number Variations of the Spanish population to the scientific/medical community.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/babelomics/SPACNACS/wiki
  download:
  - note: null
    type: Source code
    url: https://github.com/babelomics/SPACNACS
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: http://csvs.clinbioinfosspa.es/spacnacs
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2022-03-11T12:59:31.854387Z'
  license: GPL-2.0
  link: []
  maturity: null
  name: SPACNACS
  operatingSystem: []
  otherID: []
  owner: gemaroldanElixir
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Population genetics
    uri: http://edamontology.org/topic_3056
  - term: Copy number variation
    uri: http://edamontology.org/topic_3958
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2022-01-25T11:20:37.522609Z'
  biotoolsCURIE: biotools:bioexcel_building_blocks_rest_api_biobb-api
  biotoolsID: bioexcel_building_blocks_rest_api_biobb-api
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: Main developer
    orcidid: https://orcid.org/0000-0003-0513-0288
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/genis-bayarri
  - email: pau.andrio@bsc.es
    fundrefid: null
    gridid: null
    name: Pau Andrio
    note: Research Support Engineer in the Barcelona Supercomputing Center.
    orcidid: https://orcid.org/0000-0003-2116-3880
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    url: https://www.bsc.es/andrio-balado-pau
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: Research Software Engineer in the IRB-Barcelona
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  - email: gelpi@ub.edu
    fundrefid: null
    gridid: null
    name: Josep Lluís Gelpí
    note: Computational Group Manager in the BSC
    orcidid: https://orcid.org/0000-0002-0566-7723
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://www.bsc.es/gelpi-josep
  - email: null
    fundrefid: null
    gridid: null
    name: BioExcel Center of Excellence for Computational Biomolecular Research
    note: BioExcel Centre of Excellence for Computational Biomolecular Research is
      a consortium of European partners born as an H2020 project, giving support to
      academic and industrial researchers in the use of high-performance computing
      (HPC) and high-throughput computing (HTC) in biomolecular research.
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://bioexcel.eu/
  description: BioBB REST API extends and complements the BioBB library offering programmatic
    access to the collection of biomolecular simulation tools included in the BioExcel
    Building Blocks library. Molecular Dynamics setup, docking, structure modeling,
    free energy simulations, and flexibility analyses are examples of functionalities
    included in the endpoints collection. All functionalities are accessible through
    standard REST API calls, eluding the need of tools installation.
  documentation:
  - note: BioBB-API Read The Docs Documentation
    type:
    - API documentation
    - Quick start guide
    url: https://biobb-rest-api-documentation.readthedocs.io/
  download:
  - note: BioBB-API OpenAPI Documentation
    type: API specification
    url: http://mmb.irbbarcelona.org/biobb-api/rest
    version: '1.0'
  - note: BioBB-API Enpoints List
    type: API specification
    url: https://mmb.irbbarcelona.org/biobb-api/tools-documentation
    version: '1.0'
  editPermission:
    authors:
    - gelpi@ub.edu
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Spain
  elixirPlatform:
  - Interoperability
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Nucleic acid structure
        uri: http://edamontology.org/data_1459
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: netCDF
        uri: http://edamontology.org/format_3650
      - term: XTC
        uri: http://edamontology.org/format_3875
      - term: TNG
        uri: http://edamontology.org/format_3876
      - term: mdcrd
        uri: http://edamontology.org/format_3878
      - term: BinPos
        uri: http://edamontology.org/format_3885
    note: null
    operation:
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Molecular docking
      uri: http://edamontology.org/operation_0478
    - term: Nucleic acid structure prediction
      uri: http://edamontology.org/operation_0475
    - term: Nucleic acid structure analysis
      uri: http://edamontology.org/operation_2481
    - term: Structure clustering
      uri: http://edamontology.org/operation_2844
    - term: Forcefield parameterisation
      uri: http://edamontology.org/operation_3893
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Nucleic acid structure
        uri: http://edamontology.org/data_1459
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: netCDF
        uri: http://edamontology.org/format_3650
      - term: mdcrd
        uri: http://edamontology.org/format_3878
      - term: XTC
        uri: http://edamontology.org/format_3875
      - term: TNG
        uri: http://edamontology.org/format_3876
      - term: BinPos
        uri: http://edamontology.org/format_3885
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: JPG
        uri: http://edamontology.org/format_3579
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: dat
        uri: http://edamontology.org/format_1637
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: YAML
        uri: http://edamontology.org/format_3750
    - data:
        term: Structure report
        uri: http://edamontology.org/data_2085
      format:
      - term: dat
        uri: http://edamontology.org/format_1637
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: YAML
        uri: http://edamontology.org/format_3750
  homepage: https://mmb.irbbarcelona.org/biobb-api/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2022-01-25T11:38:36.888462Z'
  license: Apache-2.0
  link:
  - note: BioBB-API Landing Website
    type:
    - Other
    url: http://mmb.irbbarcelona.org/biobb-api/
  - note: BioBB-API OpenAPI Documentation
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb-api/rest
  - note: BioBB-API Endpoints List
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb-api/tools-documentation
  - note: BioBB-API Endpoints Examples
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb-api/tools-execution
  - note: BioBB-API Endpoints Tutorials
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb-api/tutorials/restapi
  - note: BioBB-API Protein MD Setup Workflow Tutorial
    type:
    - Other
    url: https://mmb.irbbarcelona.org/biobb-api/tutorials/mdsetup
  - note: BioBB-API Read-The-Docs Documentation
    type:
    - Other
    url: https://biobb-rest-api-documentation.readthedocs.io/
  maturity: Emerging
  name: BioExcel Building Blocks REST API (BioBB-API)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication: []
  relation:
  - biotoolsID: biobb
    type: uses
  toolType:
  - Web API
  - Web service
  topic:
  - term: Biomolecular simulation
    uri: http://edamontology.org/topic_3892
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2022-01-23T23:00:38.802183Z'
  biotoolsCURIE: biotools:supergnova
  biotoolsID: supergnova
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: hongyu.zhao@yale.edu
    fundrefid: null
    gridid: null
    name: Hongyu Zhao
    note: null
    orcidid: https://orcid.org/0000-0003-1195-9607
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Yiliang Zhang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Qiongshi Lu
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Yixuan Ye
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: SUPERGNOVA (SUPER GeNetic cOVariance Analyzer) is a statistical framework
    to perform local genetic covariance analysis. SUPERGNOVA only needs GWAS summary
    data and a reference panel as input data.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/qlu-lab/SUPERGNOVA/releases/tag/1.0
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Expression correlation analysis
      uri: http://edamontology.org/operation_3463
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    output: []
  homepage: https://github.com/qlu-lab/SUPERGNOVA
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2022-01-23T23:00:38.805639Z'
  license: MIT
  link: []
  maturity: null
  name: SUPERGNOVA
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1186/S13059-021-02478-W
    metadata:
      abstract: © 2021, The Author(s).Local genetic correlation quantifies the genetic
        similarity of complex traits in specific genomic regions. However, accurate
        estimation of local genetic correlation remains challenging, due to linkage
        disequilibrium in local genomic regions and sample overlap across studies.
        We introduce SUPERGNOVA, a statistical framework to estimate local genetic
        correlations using summary statistics from genome-wide association studies.
        We demonstrate that SUPERGNOVA outperforms existing methods through simulations
        and analyses of 30 complex traits. In particular, we show that the positive
        yet paradoxical genetic correlation between autism spectrum disorder and cognitive
        performance could be explained by two etiologically distinct genetic signatures
        with bidirectional local genetic correlations.
      authors:
      - name: Zhang Y.
      - name: Lu Q.
      - name: Ye Y.
      - name: Huang K.
      - name: Liu W.
      - name: Wu Y.
      - name: Zhong X.
      - name: Li B.
      - name: Yu Z.
      - name: Travers B.G.
      - name: Werling D.M.
      - name: Li J.J.
      - name: Zhao H.
      citationCount: 1
      date: '2021-12-01T00:00:00Z'
      journal: Genome Biology
      title: 'SUPERGNOVA: local genetic correlation analysis reveals heterogeneous
        etiologic sharing of complex traits'
    note: null
    pmcid: PMC8422619
    pmid: '34493297'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Exome sequencing
    uri: http://edamontology.org/topic_3676
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-02-14T08:17:30Z'
  biotoolsCURIE: biotools:VarGenius
  biotoolsID: VarGenius
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: f.musacchia@tigem.it
    fundrefid: null
    gridid: null
    name: ELIXIR-ITA-TELETHON
    note: null
    orcidid: https://orcid.org/0000-0001-9440-1080
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: VarGenius is a platform for analysis of variants from DNA sequencing
    data. Currently it can be used for WES and Panels. Starting from fastq files it
    can execute the GATK Best Practices pipeline doing both single calling and joint
    calling. Then it executes Annovar for variant annotation and generates a readable
    output in tabular and XLS format. All the data extracted from the samples (variants,
    genotypes, etc..) are uploaded into a Postgres database which can be used for
    further downstream analyses.
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://github.com/frankMusacchia/VarGenius/tree/master/GUIDE
  download:
  - note: null
    type: Source code
    url: https://github.com/frankMusacchia/VarGenius
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/frankMusacchia/VarGenius
  homepage_status: 0
  language:
  - R
  - Perl
  lastUpdate: '2021-10-08T08:49:21.521364Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://groups.google.com/forum/#!forum/VarGenius
  maturity: Mature
  name: VarGenius
  operatingSystem:
  - Linux
  otherID: []
  owner: FrankMusacchia
  publication:
  - doi: 10.1186/s12859-018-2532-4
    metadata:
      abstract: '© 2018 The Author(s).Background: Targeted resequencing has become
        the most used and cost-effective approach for identifying causative mutations
        of Mendelian diseases both for diagnostics and research purposes. Due to very
        rapid technological progress, NGS laboratories are expanding their capabilities
        to address the increasing number of analyses. Several open source tools are
        available to build a generic variant calling pipeline, but a tool able to
        simultaneously execute multiple analyses, organize, and categorize the samples
        is still missing. Results: Here we describe VarGenius, a Linux based command
        line software able to execute customizable pipelines for the analysis of multiple
        targeted resequencing data using parallel computing. VarGenius provides a
        database to store the output of the analysis (calling quality statistics,
        variant annotations, internal allelic variant frequencies) and sample information
        (personal data, genotypes, phenotypes). VarGenius can also perform the "joint
        analysis" of hundreds of samples with a single command, drastically reducing
        the time for the configuration and execution of the analysis. VarGenius executes
        the standard pipeline of the Genome Analysis Tool-Kit (GATK) best practices
        (GBP) for germinal variant calling, annotates the variants using Annovar,
        and generates a user-friendly output displaying the results through a web
        page. VarGenius has been tested on a parallel computing cluster with 52 machines
        with 120GB of RAM each. Under this configuration, a 50 M whole exome sequencing
        (WES) analysis for a family was executed in about 7h (trio or quartet); a
        joint analysis of 30 WES in about 24 h and the parallel analysis of 34 single
        samples from a 1 M panel in about 2 h. Conclusions: We developed VarGenius,
        a "master" tool that faces the increasing demand of heterogeneous NGS analyses
        and allows maximum flexibility for downstream analyses. It paves the way to
        a different kind of analysis, centered on cohorts rather than on singleton.
        Patient and variant information are stored into the database and any output
        file can be accessed programmatically. VarGenius can be used for routine analyses
        by biomedical researchers with basic Linux skills providing additional flexibility
        for computational biologists to develop their own algorithms for the comparison
        and analysis of data. The software is freely available at: https://github.com/frankMusacchia/VarGenius'
      authors:
      - name: Musacchia F.
      - name: Ciolfi A.
      - name: Mutarelli M.
      - name: Bruselles A.
      - name: Castello R.
      - name: Pinelli M.
      - name: Basu S.
      - name: Banfi S.
      - name: Casari G.
      - name: Tartaglia M.
      - name: Nigro V.
      - name: Torella A.
      - name: Esposito G.
      - name: Cappuccio G.
      - name: Mancano G.
      - name: Maitz S.
      - name: Brunetti-Pierri N.
      - name: Parenti G.
      - name: Selicorni A.
      citationCount: 8
      date: '2018-12-12T00:00:00Z'
      journal: BMC Bioinformatics
      title: VarGenius executes cohort-level DNA-seq variant calling and annotation
        and allows to manage the resulting data through a PostgreSQL database
    note: null
    pmcid: PMC6291943
    pmid: '30541431'
    type:
    - Primary
    - Benchmarking study
    version: '1.0'
  relation:
  - biotoolsID: vargenius-hzd
    type: includes
  toolType:
  - Command-line tool
  topic:
  - term: DNA mutation
    uri: http://edamontology.org/topic_2533
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2021-06-11T11:48:55Z'
  biotoolsCURIE: biotools:3drs
  biotoolsID: 3drs
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: null
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: https://www.irbbarcelona.org/en/research/adam-hospital
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/research/genis-bayarri
  description: 3DRS, a web-based tool to share interactive representations of 3D biomolecular
    structures and Molecular Dynamics trajectories
  documentation:
  - note: Read The Docs documentation
    type:
    - User manual
    url: https://3drs-documentation.readthedocs.io/en/latest/index.html
  download:
  - note: Main Web Site
    type: Other
    url: https://mmb.irbbarcelona.org/3dRS/
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Spain
  elixirPlatform:
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Nucleic acid structure
        uri: http://edamontology.org/data_1459
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: netCDF
        uri: http://edamontology.org/format_3650
      - term: BinPos
        uri: http://edamontology.org/format_3885
      - term: XTC
        uri: http://edamontology.org/format_3875
      - term: trr
        uri: http://edamontology.org/format_3910
    note: Generate animated figures for macromolecular 3D structures and trajectories
      using NGL viewer
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Trajectory visualization
      uri: http://edamontology.org/operation_3890
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://mmb.irbbarcelona.org/3dRS/
  homepage_status: 0
  language:
  - JavaScript
  - PHP
  lastUpdate: '2021-06-11T11:48:55Z'
  license: Apache-2.0
  link:
  - note: Main web server
    type:
    - Service
    url: https://mmb.irbbarcelona.org/3dRS/
  - note: GitHub repositories for the project
    type:
    - Repository
    url: https://github.com/gbayarri?tab=repositories&q=3drs
  - note: Documentation in Read The Docs
    type:
    - Other
    url: https://3drs-documentation.readthedocs.io/en/latest/
  maturity: Emerging
  name: 3DRS
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication: []
  relation:
  - biotoolsID: ngl
    type: uses
  toolType:
  - Web application
  topic:
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Biomolecular simulation
    uri: http://edamontology.org/topic_3892
  validated: 0
  version:
  - '1.0'
- accessibility: Open access (with restrictions)
  additionDate: '2020-09-14T08:41:59Z'
  biotoolsCURIE: biotools:metaxplor
  biotoolsID: metaxplor
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: guilhem.sempere@cirad.fr
    fundrefid: null
    gridid: null
    name: Guilhem Sempéré
    note: null
    orcidid: https://orcid.org/0000-0001-7429-2091
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: metaxplor@cirad.fr
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: metaXplor is an interactive viral and microbial metagenomic data manager.
    It aims at storing large volumes of user-defined sample, sequence and assignment
    information while providing a user-friendly fine-filtering web-interface. This
    online GUI also offers means to share datasets with collaborators, BLAST external
    sequences against them, and confirm assignments by running phylogenetic placement.
    metaXplor is available as a set of Docker containers that make it simple to deploy
    on various infrastructures.
  documentation:
  - note: HTML documentation is embedded in the web application
    type:
    - User manual
    url: https://metaxplor.cirad.fr/metaXplor/docIndex.jsp
  download:
  - note: This is a docker-compose file which upon execution automatically downloads
      required images
    type: Container file
    url: https://raw.githubusercontent.com/SouthGreenPlatform/metaXplor/master/docker-compose.yml
    version: 1.0-beta
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/SouthGreenPlatform/metaXplor
  homepage_status: 0
  language: []
  lastUpdate: '2021-04-22T06:15:41Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/SouthGreenPlatform/metaXplor
  - note: Live instance with public data
    type:
    - Other
    url: https://metaxplor.cirad.fr/metaXplor/
  maturity: Mature
  name: metaXplor
  operatingSystem:
  - Linux
  otherID:
  - type: rrid
    value: RRID:SCR_019025
    version: null
  owner: guilhems
  publication: []
  relation: []
  toolType:
  - Web application
  - Database portal
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - 1.0-beta
- accessibility: Open access
  additionDate: '2020-04-12T19:40:33Z'
  biotoolsCURIE: biotools:mendeliht.jl
  biotoolsID: mendeliht.jl
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Implements iterative hard thresholding as a multiple regression model
    for GWAS. Built-in support for handling PLINK and VCF files, parallel computing,
    fits a variety of GLM models, and handles group/weighting SNPs.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://openmendel.github.io/MendelIHT.jl/latest/
  download:
  - note: 'Start Julia, press ] to enter package manager mode, and type the following
      (after pkg>):


      (v1.0) pkg> add https://github.com/OpenMendel/SnpArrays.jl

      (v1.0) pkg> add https://github.com/OpenMendel/MendelSearch.jl

      (v1.0) pkg> add https://github.com/OpenMendel/MendelBase.jl

      (v1.0) pkg> add https://github.com/OpenMendel/MendelIHT.jl'
    type: API specification
    url: https://github.com/OpenMendel/MendelIHT.jl
    version: Julia 1.0-1.3
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene expression QTL analysis
      uri: http://edamontology.org/operation_3232
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  homepage: https://github.com/OpenMendel/MendelIHT.jl
  homepage_status: 0
  language:
  - Julia
  lastUpdate: '2021-04-22T05:53:16Z'
  license: MIT
  link: []
  maturity: Mature
  name: MendelIHT.jl
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: rrid
    value: RRID:SCR_018292
    version: null
  owner: biona001
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 1
  version: []
- accessibility: null
  additionDate: '2020-01-14T09:28:53Z'
  biotoolsCURIE: biotools:LyoPRONTO
  biotoolsID: LyoPRONTO
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: alexeenk@purdue.edu
    fundrefid: null
    gridid: null
    name: Alina A. Alexeenko
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'An Open-Source Lyophilization Process Optimization Tool.


    This work presents a new user-friendly lyophilization simulation and process optimization
    tool, freely available under the name LyoPRONTO. This tool comprises freezing
    and primary drying calculators, a design-space generator, and a primary drying
    optimizer. The freezing calculator performs 0D lumped capacitance modeling to
    predict the product temperature variation with time which shows reasonably good
    agreement with experimental measurements. The primary drying calculator performs
    1D heat and mass transfer analysis in a vial and predicts the drying time with
    an average deviation of 3% from experiments. The calculator is also extended to
    generate a design space over a range of chamber pressures and shelf temperatures
    to predict the most optimal setpoints for operation.'
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://drive.google.com/file/d/12is--VvE1bUGAOoNz_UvjMQ4m-SyIEO5/view
    version: '1.0'
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    output: []
  homepage: https://sites.google.com/view/rgdart/Research/lyopronto-lyophilization-processoptimization-tool
  homepage_status: 0
  language: []
  lastUpdate: '2021-01-14T08:24:30Z'
  license: null
  link: []
  maturity: null
  name: LyoPRONTO
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1208/S12249-019-1532-7
    metadata:
      abstract: © 2019, The Author(s).This work presents a new user-friendly lyophilization
        simulation and process optimization tool, freely available under the name
        LyoPRONTO. This tool comprises freezing and primary drying calculators, a
        design-space generator, and a primary drying optimizer. The freezing calculator
        performs 0D lumped capacitance modeling to predict the product temperature
        variation with time which shows reasonably good agreement with experimental
        measurements. The primary drying calculator performs 1D heat and mass transfer
        analysis in a vial and predicts the drying time with an average deviation
        of 3% from experiments. The calculator is also extended to generate a design
        space over a range of chamber pressures and shelf temperatures to predict
        the most optimal setpoints for operation. This optimal setpoint varies with
        time due to the continuously varying product resistance and is taken into
        account by the optimizer which provides varying chamber pressure and shelf
        temperature profiles as a function of time to minimize the primary drying
        time and thereby, the operational cost. The optimization results in 62% faster
        primary drying for 5% mannitol and 50% faster primary drying for 5% sucrose
        solutions when compared with typical cycle conditions. This optimization paves
        the way for the design of the next generation of lyophilizers which when coupled
        with accurate sensor networks and control systems can result in self-driving
        freeze dryers.
      authors:
      - name: Shivkumar G.
      - name: Kazarin P.S.
      - name: Strongrich A.D.
      - name: Alexeenko A.A.
      citationCount: 3
      date: '2019-11-01T00:00:00Z'
      journal: AAPS PharmSciTech
      title: 'LyoPRONTO: an Open-Source Lyophilization Process Optimization Tool'
    note: null
    pmcid: PMC6823652
    pmid: '31673810'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-01-09T17:53:02Z'
  biotoolsCURIE: biotools:VISOR
  biotoolsID: VISOR
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: davidebolognini7@gmail.com
    fundrefid: null
    gridid: null
    name: Davide Bolognini
    note: null
    orcidid: https://orcid.org/0000-0002-8735-8093
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    - Documentor
    - Developer
    url: null
  description: Haplotype-aware structural variants simulator for short, long and linked
    reads
  documentation:
  - note: null
    type:
    - User manual
    url: https://davidebolo1993.github.io/visordoc/
  download:
  - note: null
    type: Source code
    url: https://github.com/davidebolo1993/VISOR
    version: '1.0'
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode:
  - EMBL
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: VISOR {HACk, SHORtS, LASeR, XENIA} --help
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: BED
        uri: http://edamontology.org/format_3003
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Alignment
      uri: http://edamontology.org/operation_2928
    - term: Genome visualisation
      uri: http://edamontology.org/operation_3208
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://github.com/davidebolo1993/VISOR
  homepage_status: 0
  language:
  - Shell
  - R
  - Python
  lastUpdate: '2021-01-02T16:12:40Z'
  license: LGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/davidebolo1993/VISOR
  maturity: Mature
  name: VISOR
  operatingSystem: []
  otherID: []
  owner: davidebolo1993
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTZ719
    metadata:
      abstract: © 2020 Oxford University Press. All rights reserved.VISOR is a tool
        for haplotype-specific simulations of simple and complex structural variants
        (SVs). The method is applicable to haploid, diploid or higher ploidy simulations
        for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes
        at single-basepair resolution, optionally with nearby single-nucleotide variants.
        Short or long reads are drawn at random from these haplotypes using standard
        error profiles. Double-or single-stranded data can be simulated and VISOR
        supports the generation of haplotype-tagged BAM files. The tool further includes
        methods to interactively visualize simulated variants in single-stranded data.
        The versatility of VISOR is unmet by comparable tools and it lays the foundation
        to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell
        resolution.
      authors:
      - name: Bolognini D.
      - name: Sanders A.
      - name: Korbel J.O.
      - name: Magi A.
      - name: Benes V.
      - name: Rausch T.
      citationCount: 2
      date: '2020-02-15T00:00:00Z'
      journal: Bioinformatics
      title: 'VISOR: A versatile haplotype-aware structural variant simulator for
        short-and long-read sequencing'
    note: null
    pmcid: null
    pmid: '31589307'
    type:
    - Method
    version: null
  relation:
  - biotoolsID: tricolor
    type: usedBy
  toolType: []
  topic:
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: DNA structural variation
    uri: http://edamontology.org/topic_3175
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2020-05-13T16:10:08Z'
  biotoolsCURIE: biotools:retropath_rl
  biotoolsID: retropath_rl
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Mathilde Koch
    note: null
    orcidid: https://orcid.org/0000-0002-8924-3513
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Thomas Duigou
    note: null
    orcidid: https://orcid.org/0000-0002-2649-2950
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jean-Loup Faulon
    note: null
    orcidid: https://orcid.org/0000-0003-4274-2953
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: RetroPath RL performs bio-retrosynthesis using the Monte Carlo Tree
    Search Reinforcement Learning approach. It is compatible with mono-component reaction
    rules from RetroRules.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/brsynth/RetroPathRL
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/brsynth/RetroPathRL
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2020-06-16T10:55:28Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/brsynth/RetroPathRL
  maturity: Mature
  name: RetroPath RL
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: tduigou
  publication:
  - doi: 10.1021/acssynbio.9b00447
    metadata:
      abstract: © 2019 American Chemical Society.Metabolic engineering aims to produce
        chemicals of interest from living organisms, to advance toward greener chemistry.
        Despite efforts, the research and development process is still long and costly,
        and efficient computational design tools are required to explore the chemical
        biosynthetic space. Here, we propose to explore the bioretrosynthesis space
        using an artificial intelligence based approach relying on the Monte Carlo
        Tree Search reinforcement learning method, guided by chemical similarity.
        We implement this method in RetroPath RL, an open-source and modular command
        line tool. We validate it on a golden data set of 20 manually curated experimental
        pathways as well as on a larger data set of 152 successful metabolic engineering
        projects. Moreover, we provide a novel feature that suggests potential media
        supplements to complement the enzymatic synthesis plan.
      authors:
      - name: Koch M.
      - name: Duigou T.
      - name: Faulon J.-L.
      citationCount: 9
      date: '2020-01-17T00:00:00Z'
      journal: ACS Synthetic Biology
      title: Reinforcement learning for bioretrosynthesis
    note: null
    pmcid: null
    pmid: '31841626'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: retrorules
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Bioengineering
    uri: http://edamontology.org/topic_3398
  - term: Synthetic biology
    uri: http://edamontology.org/topic_3895
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2020-05-28T17:24:03Z'
  biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_command-line_workflows
  biotoolsID: bioexcel_building_blocks_tutorials_command-line_workflows
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: genis.bayarri@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Genís Bayarri
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Documentor
    - Maintainer
    url: https://www.irbbarcelona.org/en/profile/genis-bayarri
  - email: pau.andrio@bsc.es
    fundrefid: null
    gridid: null
    name: Pau Andrio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Documentor
    - Maintainer
    - Support
    url: https://www.bsc.es/andrio-balado-pau
  - email: adam.hospital@irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Adam Hospital
    note: null
    orcidid: https://orcid.org/0000-0002-8291-8071
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: BioExcel Centre of Excellence
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Provider
    url: https://bioexcel.eu/
  description: This tutorial aims to illustrate the process of building up a command-line
    workflow using the BioExcel Building Blocks library (biobb). The tutorial is based
    on the Protein Gromacs MD Setup Jupyter Notebook tutorial.
  documentation:
  - note: Read the Docs workflow documentation
    type:
    - Other
    url: https://biobb-wf-command-line.readthedocs.io/en/latest/index.html
  download:
  - note: null
    type: Source code
    url: https://github.com/bioexcel/biobb_wf_command-line
    version: '1.0'
  editPermission:
    authors:
    - gelpi@ub.edu
    - aniewielska
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    output:
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format:
      - term: trr
        uri: http://edamontology.org/format_3910
    - data:
        term: Topology data
        uri: http://edamontology.org/data_3872
      format:
      - term: GROMACS itp
        uri: http://edamontology.org/format_3883
      - term: GROMACS top
        uri: http://edamontology.org/format_3880
  homepage: http://mmb.irbbarcelona.org/biobb/availability/tutorials/command-line
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2020-06-16T10:55:28Z'
  license: Apache-2.0
  link:
  - note: Tutorial in HTML
    type:
    - Other
    url: http://mmb.irbbarcelona.org/biobb/availability/tutorials/command-line
  - note: Tutorial in Read the Docs
    type:
    - Other
    url: https://biobb-wf-command-line.readthedocs.io/en/latest/index.html
  - note: Tutorial in GitHub
    type:
    - Repository
    url: https://github.com/bioexcel/biobb_wf_command-line
  maturity: Emerging
  name: 'BioExcel Building Blocks tutorials: Command-line workflows'
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: adam.hospital@irbbarcelona.org
  publication:
  - doi: 10.1038/s41597-019-0177-4
    metadata:
      abstract: © 2019, The Author(s).In the recent years, the improvement of software
        and hardware performance has made biomolecular simulations a mature tool for
        the study of biological processes. Simulation length and the size and complexity
        of the analyzed systems make simulations both complementary and compatible
        with other bioinformatics disciplines. However, the characteristics of the
        software packages used for simulation have prevented the adoption of the technologies
        accepted in other bioinformatics fields like automated deployment systems,
        workflow orchestration, or the use of software containers. We present here
        a comprehensive exercise to bring biomolecular simulations to the “bioinformatics
        way of working”. The exercise has led to the development of the BioExcel Building
        Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an
        interoperable architecture. BioBB’s have been integrated in a chain of usual
        software management tools to generate data ontologies, documentation, installation
        packages, software containers and ways of integration with workflow managers,
        that make them usable in most computational environments.
      authors:
      - name: Andrio P.
      - name: Hospital A.
      - name: Conejero J.
      - name: Jorda L.
      - name: Del Pino M.
      - name: Codo L.
      - name: Soiland-Reyes S.
      - name: Goble C.
      - name: Lezzi D.
      - name: Badia R.M.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 4
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Data
      title: BioExcel Building Blocks, a software library for interoperable biomolecular
        simulation workflows
    note: null
    pmcid: PMC6736963
    pmid: '31506435'
    type:
    - Other
    version: Beta
  relation:
  - biotoolsID: biobb
    type: uses
  - biotoolsID: gromacs
    type: uses
  toolType:
  - Workflow
  topic:
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2020-05-29T01:36:09Z'
  biotoolsCURIE: biotools:aqmm
  biotoolsID: aqmm
  collectionID:
  - metagenome
  - metatranscriptome
  - absolute quantification
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: The AQMM was developed to perform absolute quantification of multiple
    metagenomes and it's parallel metatranscriptome. In order to use this algorithm,
    the experiment should be designed with both metagenome and metatranscriptome data.
    From the initial stage, the molecular experimental data should be recorded to
    help on estimating the overall DNA or RNA of a unit (ml/gram) of the sample. The
    AQMM was demonstrated to obtain better results of differential expression genes
    identification in comparative metatranscriptomic studies.
  documentation:
  - note: readoc document address
    type:
    - User manual
    url: https://aqmm.readthedocs.io/en/latest/
  download:
  - note: Github repo
    type: Downloads page
    url: https://github.com/biofuture/aqmm.git
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'perl ./aqmm -a <Input_metagenome_dir> -b <Input_metatranscriptome_dir> -m
      <Experimental_meta_data> -n <num_threads> -o <ouput_dir> Author Jiang Xiao-Tao
      2017-08 Email biofuture.jiang@gmail.com

      where:


      -a <Input_metagenome_dir> including all the fq files of your metagenomic samples
      after quality filtering


      -b <Input_metatranscriptome_dir> including all the paralell metatranscriptomic
      fq files with metagenomic samples after . remvoing the rRNA with tools like
      SortMeRNA.


      -m meta_data.txt including all the experimental extraction information and the
      extraction efficiency information of your sample type


      -o <ouput_dir> will include all the output results for the quantification, including
      the esimated cell numbers of metagenomic data of each sample and the estimated
      sequenced cell numbers your metatranscriptomic data included. With the quantification
      results obtained, the abundance of gene/species could be futher normalized to
      per cell/volume/gram etc. al.'
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: run the estimation
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    output:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format: []
  homepage: https://github.com/biofuture/aqmm
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2020-06-16T10:55:28Z'
  license: GPL-3.0
  link:
  - note: github page
    type:
    - Other
    url: https://github.com/biofuture/aqmm
  maturity: Mature
  name: aqmm
  operatingSystem:
  - Linux
  otherID: []
  owner: biofuture
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 1
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2019-08-09T13:04:29Z'
  biotoolsCURIE: biotools:GREIN
  biotoolsID: GREIN
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: medvedm@ucmail.uc.edu
    fundrefid: null
    gridid: null
    name: Mario Medvedovic
    note: null
    orcidid: https://orcid.org/0000-0003-4510-3102
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Interactive Web Platform for Re-analyzing Gene Expression Omnibus (GEO)  RNA-seq
    Data.
  documentation:
  - note: null
    type:
    - General
    url: http://www.ilincs.org/apps/grein/?gse=
  download:
  - note: null
    type: Container file
    url: https://hub.docker.com/r/ucbd2k/grein
    version: null
  - note: null
    type: Source code
    url: https://github.com/uc-bd2k/GREIN/releases/tag/1.0
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Differential gene expression analysis
      uri: http://edamontology.org/operation_3223
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    output: []
  homepage: https://shiny.ilincs.org/grein
  homepage_status: 0
  language:
  - R
  lastUpdate: '2020-06-16T10:55:25Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/uc-bd2k/grein
  - note: null
    type:
    - Issue tracker
    url: https://github.com/uc-bd2k/grein/issues
  maturity: Mature
  name: GREIN
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hans
  publication:
  - doi: 10.1038/S41598-019-43935-8
    metadata:
      abstract: '© 2019, The Author(s).The vast amount of RNA-seq data deposited in
        Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly
        underutilized resource for biomedical research. To remove technical roadblocks
        for reusing these data, we have developed a web-application GREIN (GEO RNA-seq
        Experiments Interactive Navigator) which provides user-friendly interfaces
        to manipulate and analyze GEO RNA-seq data. GREIN is powered by the back-end
        computational pipeline for uniform processing of RNA-seq data and the large
        number (>6,500) of already processed datasets. The front-end user interfaces
        provide a wealth of user-analytics options including sub-setting and downloading
        processed data, interactive visualization, statistical power analyses, construction
        of differential gene expression signatures and their comprehensive functional
        characterization, and connectivity analysis with LINCS L1000 data. The combination
        of the massive amount of back-end data and front-end analytics options driven
        by user-friendly interfaces makes GREIN a unique open-source resource for
        re-using GEO RNA-seq data. GREIN is accessible at: https://shiny.ilincs.org/grein,
        the source code at: https://github.com/uc-bd2k/grein, and the Docker container
        at: https://hub.docker.com/r/ucbd2k/grein.'
      authors:
      - name: Mahi N.A.
      - name: Najafabadi M.F.
      - name: Pilarczyk M.
      - name: Kouril M.
      - name: Medvedovic M.
      citationCount: 25
      date: '2019-12-01T00:00:00Z'
      journal: Scientific Reports
      title: 'GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data'
    note: null
    pmcid: PMC6527554
    pmid: '31110304'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-06-18T19:35:41Z'
  biotoolsCURIE: biotools:ComplexBrowser
  biotoolsID: ComplexBrowser
  collectionID:
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: veits@bmb.sdu.dk
    fundrefid: null
    gridid: null
    name: Veit Schwämmle
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: ComplexBrowser is a R based software for supervised analysis of changes
    in protein complex abundance and subunit co-expression in proteomic datasets.
    It uses information contained in CORUM and EBI Complex Portal databases to provide
    the user with visualizations helping with biological interpretation of obtained
    results. ComplexBrowser also incorporates a normalization and quality control
    steps.
  documentation:
  - note: null
    type:
    - User manual
    url: https://bitbucket.org/michalakw/complexbrowser/raw/dc9d8f0c8dff610e2f58e3cb5f5087d050df26f2/Manual.pdf
  download:
  - note: null
    type: Source code
    url: https://bitbucket.org/michalakw/complexbrowser/
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Principal component visualisation
      uri: http://edamontology.org/operation_2939
    - term: ID mapping
      uri: http://edamontology.org/operation_3282
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Dendrogram visualisation
      uri: http://edamontology.org/operation_2938
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    - term: Protein interaction network analysis
      uri: http://edamontology.org/operation_0276
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Expression correlation analysis
      uri: http://edamontology.org/operation_3463
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: png
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: http://computproteomics.bmb.sdu.dk/Apps/ComplexBrowser/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2020-06-16T10:55:23Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://computproteomics.bmb.sdu.dk/
  maturity: null
  name: ComplexBrowser
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: vtsiamis
  publication:
  - doi: 10.1101/573774
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2017-09-11T15:08:17Z'
  biotoolsCURIE: biotools:miolite
  biotoolsID: miolite
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: mklapa@iceht.forth.gr
    fundrefid: null
    gridid: null
    name: Maria Klapa
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://miolite2.iceht.forth.gr
  description: The MESBL GC-MS metabolite peak database is a standardized library
    of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating
    the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic
    Engineering and Systems Biology Laboratory, Greece, appropriately filtered GOLM
    database peak information and Human Metabolome database information.
  documentation:
  - note: The website provides information about citing the respective tool and how
      to contact the developer for obtaining the database.
    type:
    - General
    url: http://miolite2.iceht.forth.gr
  download:
  - note: List is incorporated in the M-IOLITE software but can also be obtained as
      a separate file upon request.
    type: Downloads page
    url: http://miolite2.iceht.forth.gr
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output: []
  homepage: http://miolite2.iceht.forth.gr
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2019-07-26T16:58:29Z'
  license: null
  link:
  - note: The download website
    type:
    - Other
    url: http://miolite2.iceht.forth.gr
  maturity: null
  name: MESBL GC-MS metabolite peak database
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: mklapa
  publication:
  - doi: 10.1016/j.ifacol.2016.12.140
    metadata:
      abstract: © 2016Metabolomics, as a rapidly growing omic analysis, has being
        used extensively to explore the dynamic response of biological systems in
        several diseases/disorders and contexts. Therefore, it has become commonplace
        in a wide variety of disciplines and there is an intense need for development
        of software suites that provide the user with a less complicated and invalid
        analysis. These suites must integrate meta-analysis, a standardized data normalization
        method and a safe repository for all types of biological samples. In the case
        of the Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics, due to the
        complexity of the analysis, multiple procedures that are essential for the
        metabolite identification require special manipulation. Moreover, metabolomic
        analysis produces a vast amount of unidentified compound data, so there is
        a need for unknown peak identification methods. While a number of tools offer
        access to datasets, constantly providing new releases for data processing
        and the fact that considerable progress has been made in that area, there
        is no computational platform that emerges as a standardized approach which
        includes specialized normalization methods for GC-MS metabolomic analysis
        and incorporates the metabolic network analysis into data interpretation and
        unknown peak identification. To address these issues, as the datasets obtained
        from metabolomics experiments still remain extremely large and dense, we have
        implemented M-IOLITE, a computational suite for the efficient and automatic
        analysis of high-throughput metabolomic experiments. The aim of the suite
        is to streamline GC-MS metabolomic data analysis and to reduce complexity
        enabling the use of a friendly interface for processing, validating and annotating
        data. It integrates specialized normalization methods, a safe data repository
        and a peak library providing through its pipeline a useful tool which enables
        rapid and accurate analysis of the metabolomic profiles into an interactive
        system.
      authors:
      - name: Maga-Nteve C.
      - name: Klapa M.I.
      citationCount: 7
      date: '2016-01-01T00:00:00Z'
      journal: IFAC-PapersOnLine
      title: Streamlining GC-MS metabolomic analysis using the M-IOLITE software suite
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation:
  - biotoolsID: m-iolite
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 1
  version:
  - '1.0'
next: null
previous: null
